Despite keeping Defense Secretary Robert Gates in the Pentagon, President-elect Obama’s transition team informed 90 Bush appointees their services will not be needed after Inauguration Day.

Scott Gration, a senior official on Obama’s transition team, called and emailed several of President Bush’s Pentagon appointees about 10 days ago to inform them they were being dismissed.

A spokesman for the Pentagon said Gates was "absolutely satisfied" with the way the transition was handled.

Gates "is sensitive to the fact that a number of appointees will not be able to stay on after [Jan.] 20th," Defense Department spokesman Geoff Morrell said. He noted Gates did request many appointees stay on and the "Obama team was able to cooperate."

But O'Beirne made it clear in the email that in some cases of dismissal, he thinks the employee's politics played a role in their being let go.

O'Beirne said that Gates had "sought to keep virtually his entire team in place pending the availability of Obama replacements."

Out of roughly 250 political appointees, 90 were dismissed.

"Whatever negotiations occurred in pursuit of that goal, the Gration notifications evidently reflected the results of those efforts," O'Beirne wrote.

Traditionally political appointees resign at the end of a president’s term, leaving the new commander in chief to put his own team in place but with Gates staying in the top Pentagon job there was reason to believe many of his staff would also stay.

The Obama team noted that a majority of the political appointees will remain in place.

"Given that our nation is at war, we have asked several political appointees at the Department of Defense to stay in their jobs past January 20th to help ensure a smooth transition. We are grateful for the cooperation and professionalism of the men and women at the Department of Defense in support of our men and women in uniform," an Obama transition official said.

Bush has repeatedly stated that he wanted to see an orderly transition to ensure that the next president would hit the ground running at a time when the country is fighting two wars and weathering one of the most significant economic crises in modern times.

Until now, that process seemed to be going smoothly as a number of departments have reported efficient and even cordial working relationships between Bush appointees and transition officials. The O'Beirne email is the first sign of discontent.

In the email, O'Beirne tried to assure the soon-to-be displaced employees that the decisions were based on "policy change in the Obama administration" and not based on performance.

However, he said, if employees "harbor residual doubts" then they can "content yourself with the likelihood that it was your outstanding performance as a Bush appointee that drew the opposition's attention to you."

"In that regard, you may take justifiable satisfaction that you were among the first to be chosen," O'Beirne wrote.

Other reasons O'Beirne cited for employees' dismissal were "politics, matter of policy and availability of qualified replacements and the strength of the permanent career and uniformed staffs."

Morrell, a political appointee who is staying at the Pentagon, noted that while O'Beirne is usually the liaison for political appointees Gates chief of staff Robert Rangel has taken over that role. Rangel is also staying on. 

"Jim has had to defer many of the things he could normally respond to," Morrell said as a possible explanation for the email.

-- Emily Goodin contributed to this article.

This article was updated at 8:07 p.m.