American officials said that it appeared that the weapons found in Turkey were given to Iraqi units in 2004 and 2005 when, in the rush to build police and army units, controls on distribution of firearms had been much weaker. Gen. David H. Petraeus, who was then in charge of training and equipping Iraqi forces and who is now the top American commander in Iraq, has said that the imperative to provide weapons to Iraqi security forces was more important at the time than maintaining impeccable records.

By checking serial numbers, American officials confirmed that some of the recovered weapons, which included handguns made by Glock, an Austrian weapons manufacturer, had originally been bought by the Defense Department for distribution in Iraq, the officials said.

Geoff Morrell, a Pentagon spokesman, said at a briefing on Wednesday that Mr. Gates was “deeply troubled by the reports and allegations” about problems accounting for American-supplied weapons in Iraq.

Pentagon officials said Wednesday that the problem of weapons turning up in Turkey was part of a larger investigation being carried out by the Pentagon inspector general, Claude M. Kicklighter, a retired Army three-star general, into allegations that American-supplied weapons had been improperly accounted for and fallen into the wrong hands.

“General Kicklighter has informed the secretary that he will remain in-country as long as it takes to find out if record-keeping problems persist, and if so, make recommendations to the commanders on the ground how to fix those problems,” Mr. Morrell said.

American officials added that they had not seen firm evidence that the firearms had been found in the hands of Kurdish separatists from the outlawed Kurdistan Workers Party, the hard-line Kurdish separatist group that for years has used northern Iraq as a sanctuary to carry out attacks inside Turkey.

Turkish officials have complained in recent months that Kurdish officials in senior positions in the Iraqi government, including Massoud Barzani, the president of the Kurdistan region, are actively supporting the Kurdish Workers Party, known as the PKK. Mr. Barzani and other Kurdish officials say they do not support attacks by the PKK into Turkey.