Israel’s Defense Ministry apologized on Monday for forcing a pregnant New York Times photographer to remove her clothes and submit to a physical search after she had already passed through an X-ray machine three times at a checkpoint in Gaza last month.

The photographer, Lynsey Addario, is a Pulitzer Prize-winning war photographer who was one of four Times journalists subjected to brutal treatment in March after being captured by Libyan government forces and held for six days.

In a letter to the Israeli ministry last month, Ms. Addario wrote that soldiers at the Erez Crossing in northern Gaza had treated her with “blatant cruelty” when she arrived there on Oct. 24 and asked not to have to pass through the X-ray machine. Because she was seven months pregnant at the time, she had been advised by her obstetrician to avoid exposure to radiation.

Ms. Addario had phoned an official at the border crossing in advance to make her request and had been assured that there would be no problem. When she arrived at the checkpoint, however, she was told that if she did not pass through the X-ray machine, she would have to remove all of her clothes down to her underwear for a search. To “avoid the humiliation,” Ms. Addario decided to pass through the X-ray machine.

“As I passed through,” she wrote, “a handful of soldiers watched from the glass above the machine smiling triumphantly. They proceeded to say there was a ‘problem’ with the initial scan, and made me pass through two additional times as they watched and laughed from above. I expressed each time that I was concerned with the effect the radiation would have on my pregnancy.”

She added:

After three passes through the X-ray, I was then brought into a room where a woman proceeded to ask me to take off my pants. She [asked me to lift] up my shirt to expose my entire body while I stood in my underwear. I asked if this was necessary after the three machine checks, and she told me it was “procedure” — which I am quite sure it is not. They were unprofessional for soldiers from any nation.

In an e-mail to the head of Israel’s government press office on Monday, the Defense Ministry wrote that after “a deep and serious investigation into the matter of Ms. Addario’s security check last month,” it had concluded that her request to avoid the machine had not been passed on to the security officials at the checkpoint because of “faulty coordination between the parties involved.”

Although the statement said, “We would like to apologize for this particular mishap in coordination and any trouble it may subsequently have caused to those involved,” the ministry dismissed Ms. Addario’s concern about radiation. “The relevant machine is situated at numerous borders and airports across the world and presents no danger for those who use it,” the statement said.

The ministry added that although the search “was carried out according to the accepted security procedure,” officials have “decided to hone the procedure for foreign journalists.”

Ethan Bronner, the Jerusalem bureau chief of The Times, said in response to the statement:

The Times remains shocked at the treatment Lynsey Addario received and shocked at how long the investigation has taken since our complaint was lodged a month ago. The careless and mocking way in which she was handled should not be considered accepted security procedure. We welcome the announcement by the Defense Ministry of plans to hone that procedure.

In a message posted on Twitter on Monday night, Ms. Addario’s husband, Paul de Bendern, referred to the incident as one of “terrible humiliation for my pregnant wife.”

Ms. Addario’s experience came nine months after a pregnant Arab-Israeli journalist working for Al Jazeera was denied entry to a cocktail party hosted by the Israeli government because she agreed to take off some of her clothes for a security check but refused to remove her bra. Before the same event, other journalists, including the bureau chief of The Wall Street Journal, were also strip-searched.