Facilities in Virginia and West Virginia told Reuters they were forced to shutter primary care clinics or lay off staff.
Other community health clinics in California and Virginia said they received notices of termination for federal grants that support HIV prevention care.
Some of the funding was cancelled following Trump administration orders for the federal government to scrap diversity, gender and inclusion programs and to recognise only two sexes – male and female.
Others appear related to a freeze on federal funding that was rescinded last week.
"There is mass confusion. We expect that interruption will grow if there is not clarity from federal agencies in the coming hours and days," said David C. Harvey, executive director of the National Coalition of STD Directors, an organisation representing providers of sexually transmitted disease prevention programs and services.
"This is money that pays for staff payroll, rent and healthcare supplies."
Officials at the Department of Health and Human Services did not immediately respond to a request for comment.
Three community health centres near Richmond, Virginia, were forced to shut down after federal funds used to pay staff salaries remained inaccessible since last week, said Virginia Community Healthcare Association spokesperson Joe Stevens.
As of Friday, another nine centres across Virginia also could not access federal funds but continued to see patients by tapping into reserve funds.
"They will need money in the next week," said Stevens.
"We don't know why some centres can access funds and some cannot."
In Virginia, community health centres provide medical, dental, behavioural health, pharmaceutical and substance use services for approximately 400,000 patients.
For much of the state's rural areas, the centres are the only option for primary care, said Stevens.
One centre that was still unable to access federal funds is in southwestern Virginia, where the next closest option for medical care is more than an hour's drive, he said.
Most providers were able to access Medicaid and grant monies once the spending freeze was rescinded.
However, some say they are still cut off from payments used for essential care, including medical, dental, prescription drugs and behavioural health.
"It is literally changing moment to moment," said Alison Barkoff, an expert on disability rights and health law and policy professor at George Washington University.
The Appalachian centre for Independent Living, based in Charleston, West Virginia, was cut off for more than a week.
The delay forced the disability services and support organisation to lay off three out of five staff members.
The centre offered to rehire the employees after its access to federal funding resumed.
"We don't have any other choice but to push through and do what we need to do to keep the centre running," said Pride.
Late last week, some healthcare centres that provide HIV prevention services and care for transgender patients received notices that grants issued by the US Centres for Disease Control and Prevention would be terminated.
The letters cited the Trump administration's orders on diversity and gender identity, according to three recipients of the notices.
A spokesperson for the US Centres for Disease Control and Prevention referred questions about the grants to the Department of Health and Human Services.
St. John's Well Child and Family Centre, a network of public health centres in South and Central Los Angeles, cannot access $US746,000 ($A1.2 million) remaining from a $US1.6 million ($A2.6 million) grant used to provide prevention, testing and treatment for about 500 transgender people at risk of HIV, sexually transmitted infections, tuberculosis and hepatitis C.
"We have made a decision not to cut back any programs because of any threats from the federal government," said St. John's President Jim Mangia.
St. John's has joined a lawsuit filed by California's attorney general contesting the funding cuts.
Mangia says he will seek private funding to make up the loss.
