Just a small percentage of the hundreds of thousands of migrants processed by the U.S. this year have received COVID-19 vaccinations while in federal custody, and half of them are unaccompanied children, according to unpublished government data obtained by CBS News.

Collectively, U.S. Immigration and Customs Enforcement (ICE) and the Department of Health and Human Services (HHS) have administered vaccine doses to more than 90,000 immigrants in deportation proceedings, the statistics show.

For months, however, Customs and Border Protection (CBP) declined to offer vaccines, leaving hundreds of thousands at risk of being unvaccinated when they were deported or released into the U.S. Since January, CBP has processed migrants along the southern border over 1.6 million times, agency data shows.

Unlike other federal agencies, CBP resisted calls from public health experts to vaccinate migrants in its custody, despite internal plans to do so dating back to the summer.

As part of a proposal to unwind a Trump-era policy that has allowed the U.S. to expel migrants during the pandemic, CBP was tasked with developing a plan by July 31 to vaccinate migrants, an internal memo obtained by CBS News shows. Its intent was for “all willing adult members of families” to be vaccinated.

But senior White House and DHS officials backtracked on winding down the expulsion policy, known as Title 42, due to concerns about the spread of the Delta variant and the political pressure faced by the administration over the high number of border crossings, Biden appointees familiar with the plan said.

It was only until this week that the Department of Homeland Security announced that CBP intends to offer vaccines to some migrants returned to Mexican border cities under the Remain in Mexico program, a Trump-era policy that a federal court ordered the Biden administration to reinstate.

The policy change had been demanded by the Mexican government, which said the U.S. could help contain the coronavirus on both sides of the border by vaccinating migrants.

Public health experts have strongly criticized CBP’s current policy. 

“Denying vaccine access to this population is incredibly thoughtless and dangerous, for the individuals themselves and for anyone who comes in contact with them,” said Dr. Ranit Mishori, a Georgetown University professor and Physicians for Human Rights adviser, pointing to the ample U.S. vaccine supply.

Unlike CBP, the other two government agencies that detain or house migrants in federal custody have been offering vaccination for months.

In the spring, ICE started offering coronavirus vaccines to immigrants held in its long-term adult detention centers. As of November 29, more than 44,000 immigrants have received at least one shot of the vaccine while in ICE custody, according to agency figures. 

At least 21,970 immigrants detained by ICE have declined to be vaccinated, the statistics show. In addition to holding recent border-crossers and asylum-seekers, ICE detains other immigrants the government seeks to deport, including permanent residents convicted of certain crimes.

So far, 46,480 migrant children have received at least one dose of the COVID-19 vaccine while in the custody of the Office of Refugee Resettlement, which cares for minors who cross the southern border without their parents. The HHS agency began offering vaccination to eligible unaccompanied teenagers in June.

As of Wednesday, 8,090 unaccompanied children had received two doses of the vaccine. Minors who have received only one dose can be released to sponsors, who are supposed to receive information on how the children can get a second shot in their new communities.

Migrants exit a Border Patrol bus and prepare to be received by the Val Verde Humanitarian Coalition after crossing the Rio Grande on September 22, 2021, in Del Rio, Texas.

BRANDON BELL / Getty Images

Unlike ICE detention facilities and HHS shelters, Border Patrol facilities are designed to hold migrants for no longer than three days — which the agency has previously cited as a reason for not providing vaccines to migrants.

But in the June plan to wind down the Title 42 expulsions, DHS officials said Border Patrol could use single-dose vaccines. “Providing Johnson and Johnson vaccines in CBP facilities is likely to be less onerous than testing,” the memo said.

The exact reasons why CBP did not move forward with plans to vaccinate migrants earlier this year remain unclear. But the internal DHS memo suggested that “vaccinations may be viewed as a draw to crossing the border without authorization.”

Public health experts, advocates for asylum-seekers, United Nations officials and the Mexican government have urged the U.S. to vaccinate migrants, saying efforts to contain the coronavirus should include everyone, including new arrivals who don’t have legal status.

“For the benefit of migrants, for the benefit of communities in home countries and the U.S., we want to increase vaccination,” Megan Coffee, an infectious disease physician and professor at Columbia University, told CBS News, highlighting the uncertainty around the newly discovered Omicron variant. “Viruses don’t care about people’s statuses.”

Last month, Felipe González, the United Nations Special Rapporteur on the Human Rights of Migrants, said it would be a “grave violation of the human rights of migrants” for the U.S. to deny them vaccines as a matter of immigration policy. 

While acknowledging that Border Patrol has not yet provided vaccinations, DHS officials noted the department has other protocols in place to mitigate the spread of the coronavirus, including a Border Patrol requirement that migrants wear face masks “at all times.”

The department has also set up a system to test migrants who are not expelled to Mexico or their home country under the emergency Title 42 policy. 

Unaccompanied children, whom the Biden administration exempted from the Title 42 expulsions, are tested at least twice for the coronavirus after being transferred to HHS housing facilities. Migrant adults transferred to long-term ICE detention facilities are also tested at intake.

While some families with children continue to be expelled, the vast majority have been allowed to stay in the U.S. in recent months while their cases are adjudicated. On the other hand, U.S. border officials have expelled 82% of the single adult migrants they have encountered since January, according to CBP figures.

In most areas of the southern border, DHS has relied on local jurisdictions and groups, including faith-based shelters, to provide coronavirus testing to migrant families and adults who are released from U.S. custody. In more remote areas, including Del Rio, Texas, ICE officials have been testing migrants.

DHS noted that some of the groups testing migrants for the coronavirus may also offer them vaccination.

Rubén Garcia, the director of the Annunciation House, the largest network of migrant shelters in El Paso, said his group is offering vaccines at one site. Some migrants, Garcia noted, have declined the vaccine, citing concerns about getting side effects during their travels to their respective destinations in the U.S.

But Garcia said the U.S. government should be taking the lead in vaccinating migrants. Specifically, he said the U.S. should set up vaccination centers in El Paso for migrants and Ciudad Juárez residents who want to get vaccinated, just like it did for Mexican factory workers earlier this year.

“What you are really talking about is the pandemic,” Garcia said. “We’re not talking about immigration law. We’re not talking about politics. We’re simply saying we want to get as many people vaccinated.”