Over the summer, Royal Philips NV set off a scramble among sleep apnea sufferers when it recalled millions of machines that many use to breathe at night, citing concerns that the foam in the devices could pose a health risk.

Last week, users were thrown another curveball when the Food and Drug Administration warned the replacement machines that the Dutch health giant has been cranking out since September may be harmful, too. The FDA didn’t order a recall of some 250,000 replacement devices Philips has sent to users, but said...

Over the summer, Royal Philips NV set off a scramble among sleep apnea sufferers when it recalled millions of machines that many use to breathe at night, citing concerns that the foam in the devices could pose a health risk.

Last week, users were thrown another curveball when the Food and Drug Administration warned the replacement machines that the Dutch health giant has been cranking out since September may be harmful, too. The FDA didn’t order a recall of some 250,000 replacement devices Philips has sent to users, but said it was concerned that a silicone-based foam used in the substitute devices could emit harmful gases. That has raised new questions among users about what to do.

“It is disappointing and frustrating,” said Paula Martin, of Laramie, Wyo., who received her new device in October. “I feel like they should be able to give me something that is safe, and I should be assured that it’s safe.”

Critics blame Philips for a lack of communication about the problems with the old devices and now the new ones. Over the summer, users scrambled to secure alternative devices, which suddenly became in short supply. Doctors and so-called durable medical equipment providers, or DMEs, that essentially act like pharmacies for many doctor-prescribed devices, didn’t have answers.

Philips has said it takes the matter seriously and is cooperating fully with the FDA.

The recall wasn’t limited to the U.S., leaving millions of users across Europe and elsewhere in the dark about what to do as well. The company in June recalled as many as 4 million devices, about half of which were in the U.S. It cited concerns that a sound-damping foam inside the machine could be harming users. The foam is made of a material called polyester-based polyurethane, or PE-PUR, that Philips said can degrade and be inhaled by the user. It can also emit harmful gases, which along with the particles could be carcinogenic, according to the recall notice.

Most of the devices affected by the recall are so-called CPAP and BiPAP machines, devices which regulate breathing by gently pushing air into the lungs through a mask. They are primarily used to treat sleep apnea, a condition that causes sufferers to stop breathing for brief periods while asleep. The recall also affects some ventilators.

Philips promised to repair or replace affected devices but only started doing so in September after the FDA approved its rework plan. It expects to repair or replace all affected machines within a year. Some users have turned to Philips’s major competitor ResMed Inc. Others bought old machines secondhand or ripped the foam out themselves.

The FDA’s latest concerns, which it made public Friday, surfaced during a recent inspection of the Murrysville, Pa., facility where Philips makes its CPAP and BiPAP machines. Inspectors discovered that a similar device sold outside the U.S., which also uses silicone-based foam, failed a safety test because it released potentially harmful gases.

The agency’s approval of the silicone-based foam for the repair-and-replace program was based on testing provided by Philips that showed acceptable results. The FDA has asked Philips to hire an independent laboratory to run further tests on devices that use the silicone-based foam to identify any potential safety risks.

The FDA said it would await the results of that testing to conclude whether the silicone-based foam poses any risk to patients. Philips said it would continue to send out replacement machines.

Meanwhile, the FDA recommends that patients continue to use devices containing the silicone-based foam, because it would be more harmful to stop treatment altogether. Without treatment, sleep apnea sufferers can go on to develop serious long-term conditions such as high blood pressure, stroke, diabetes and heart problems. The sleep deprivation associated with untreated sleep apnea also has been associated with road traffic accidents.

Ms. Martin, 50 years old, said she used her original CPAP machine until receiving the replacement, and will continue to use the replacement device. “I know what not getting good sleep and sleep apnea does to my lifespan,” she said.

Melvyn Ball, 74 years old, received his replacement device in October but found that it gave off a strong smell that gave him a headache and nausea. He doesn’t know whether the smell is linked to the silicone-based foam. For now, he has gone back to his original CPAP machine with the PE-PUR foam. “I am worried, I am anxious about whether this is making me sicker, but I also have to deal with the fact I need this to sleep at night,” said Mr. Ball, who lives in Merrimac, Mass.

The FDA report detailed findings suggesting that the company had for years taken inadequate action in response to complaints relating to foam degradation. Philips’s share fell sharply on the Monday after the FDA’s Friday report.

Philips Chief Executive Frans van Houten said in a statement that the company is in discussions with the FDA regarding the report’s findings. Under FDA rules, Philips has 15 working days from the report date, Nov. 9, to respond. “We remain fully committed to supporting the community of patients who rely on the affected devices, and the physicians and customers who are dedicated to meeting patient needs,” he added.