Walgreens has inoculated hundreds of thousands of Americans against COVID-19 this year using the vaccine developed by Pfizer and Germany’s BioNTech. But the pharmacy chain has not been following guidance from federal health officials about the timing of second doses.

People are supposed to get two doses, three weeks apart. Walgreens, however, separated them by four weeks because that made it faster and simpler for the company to schedule appointments.

There is no evidence that separating the doses by an extra week decreases the vaccine’s effectiveness. While the Centers for Disease Control and Prevention recommends a three-week gap, the agency says it is acceptable to separate the doses by up to six weeks if necessary.

But Walgreens’ decision, which it didn’t publicly announce, confused some customers and caught the attention of federal health officials. Kate Grusich, a CDC spokeswoman, said the agency had asked Walgreens to stop using a longer-than-recommended time period between doses.

The company’s vaccine-scheduling system by default schedules all second doses four weeks after the first. Doses of Moderna’s vaccine, which Walgreens is also administering, are supposed to be spaced four weeks apart. Using the same gap for both vaccines was “the easiest way to stand up the process based on our capabilities at the time,” said Dr. Kevin Ban, Walgreens’ chief medical officer.

Now Walgreens is changing its system. Starting as soon as the end of the week, the pharmacy will automatically schedule people for Pfizer doses three weeks apart, Ban said.

Walgreens is one of the largest among dozens of drugstore and grocery store chains that are giving out vaccines allocated by states and via a federal program that the White House said last week would expand to 40,000 locations. Walgreens reported last week that it had given out more than 8 million COVID vaccine doses, including 4 million in March, and expects to give out 26 million to 34 million before the end of August.

Walgreens, along with CVS, previously led an effort to vaccinate nursing homes and other long-term care facilities, during which the chain gave out Pfizer doses at facilities with visits spaced three weeks apart.

The vaccination campaign is a business opportunity for Walgreens, which is bringing in revenue from the vaccine administration fees paid by government and private payers as well as from purchases made by shoppers coming in for vaccines. The company requires people to create a Walgreens account to search online for a vaccine appointment.

Most other major pharmacies, including CVS and Rite Aid, stuck with the CDC’s guidance on the timing of second doses. CVS, for example, schedules second Pfizer shots for 20 to 23 days after the first shot, said T.J. Crawford, a spokesman for the chain.

Some public health experts believe the U.S. should delay the second doses of vaccines by longer than Walgreens has been doing with the Pfizer vaccine. That way, more people can get partial protection through the first shots.

But it was a three-week gap that underwent extensive clinical testing, and U.S. officials and Pfizer executives have not voiced support for alternate dosing schedules.

Asked about Walgreens’ scheduling, Kit Longley, a spokesman for Pfizer, said the safety and efficacy of the company’s vaccine had not been evaluated on dosing schedules different from the three-week gap tested in clinical trial volunteers.