The Trump administration has asked researchers and organizations whose work is conducted overseas to disclose ties to those regarded as hostile, including “entities associated with communist, socialist or totalitarian parties,” according to a questionnaire obtained by The New York Times.

The online survey was sent this week to groups working abroad to research diseases like H.I.V., gather surveillance data and strengthen public health systems. Recipients received funding from the Centers for Disease Control and Prevention, the United States Agency for International Development and other federal sources.

The questionnaire appears to be very similar to one sent earlier this week to partners of the United States Agency for International Development, which has been all but dismantled by the Trump administration. Both were titled “Foreign Assistance Review.”

Recipients were instructed to respond within 48 hours. Some grantees interviewed by The Times feared that impolitic or unsatisfactory answers could lead to cancellation of funding.

“Taxpayer dollars must not fund dependency, socialism, corrupt regimes that oppose free enterprise, or intervene in internal matters of another sovereign nation,” the questionnaire said.

“A truly prosperous America prioritizes domestic growth, innovation, and economic strength over foreign handouts,” it added.

A spokesman for the White House did not return a request for comment about the survey.

The form asks a series of questions that touch on collaborators, including whether grant recipients work with drug cartels or “groups that promote mass migration.”

It asks about the impact of programs, such as whether they have an effect on “promoting religious freedom and combating Christian persecution” in other nations.

It asks grant recipients if they or their organizations collaborate with or have received funding from Russia, Cuba, Iran or China — including the Confucius Institute, which works with China’s Ministry of Education to promote language and cultural exchanges with American students.

Some federal officials who oversee grants said they were particularly dismayed by a question asking grantees to disavow associations with communist entities. The United States assists with health work in a number of communist countries, including Vietnam.

“Some of my grantees are literally the public health government structures in a communist country,” said one federal official, who spoke anonymously for fear of retribution. “This is painful.”

Awards and contracts to aid groups have been under review during a 90-day pause on foreign aid, but in some instances they have been canceled and restored over the past few weeks. The Supreme Court on Wednesday ordered the federal government to resume the payments.

Various versions of the questionnaires were sent out starting Wednesday, and the deadlines appear to range from midnight on Friday to 5 p.m. Monday. But the process has been riddled with confusion.

Some grantees appear to have been given extensions, while others were denied. Some noted that the deadline seemed to shift as more copies of the questionnaire were received each day.

The recipients included scientists at large universities and research programs in the United States, as well as tiny organizations abroad. Some questionnaires were apparently sent in error; one was received by Maine’s health department.

A principal investigator with two C.D.C. grants for domestic research projects received the email Thursday evening, only to receive another Friday morning telling him to ignore the previous missive.

The answers are meant to be filled out by a single person in one sitting, with no way to save responses for a break. The form estimates the task to take 30 minutes, including the time required for gathering the necessary data and documents.

“The chaotic way in which these stop work orders, terminations, waivers, reinstated awards, surveys — all with rapid deadlines and minimal communication — have been sent is distracting and incredibly disruptive,” said one scientist, who spoke anonymously for fear of losing funding.

Some American grantees have turned to lawyers for advice about how to phrase the responses.

Organizations that are based overseas are most at a disadvantage. The communications pause the Trump administration imposed several weeks ago still prevents them from talking to federal officials who might be able to assist, according to one C.D.C. official.

Grantees are allowed only to talk to American officials in the countries where they are based.

“They could lose the vital funds they need to do their work if they don’t answer these questions appropriately,” said a federal official, who spoke anonymously for fear of retribution.