Scott Gration, a senior official on Obama's transition team, called and e-mailed several of President George Bush's Defense Department appointees about 10 days ago, telling them they were being let go, The Hill reported.
Jim O'Beirne, special assistant to the Defense secretary, followed up Gration's e-mail, expressing frustration that Gration informed the employees directly instead of alerting O'Beirne's office first.
"With regard to the process, I am unable to provide an explanation," O'Beirne wrote in the e-mail obtained by The Hill and published Tuesday. "I played no part in it, and I will not speculate why matters were handled as they were."
A Pentagon spokesman said Defense Secretary Robert Gates, who is staying with Obama, was "absolutely satisfied" with the way the transition was handled.
Gates requested that many appointees stay on and the "Obama team was able to cooperate," Defense Department spokesman Geoff Morrell said.
The Pentagon has about 250 political appointees.