In an April 7 e-mail, Robert Rangel, special assistant to Defense Secretary Robert Gates, gave all Bush holdovers until the close of business on Friday to sign the agreement, which puts restrictions on post-government employment.
Politicos who refuse to comply will be required to leave their position by the end of April.
"Those who choose not to sign the ethics pledge and leave before April 30, 2009 (or those who choose to sign the pledge and are replaced after April 30, 2009), will be asked to submit their resignations, and the department will treat their separations as involuntary," Rangel wrote.
In December, Rangel asked political appointees to remain at the department until the new administration made a decision regarding their status. But in a Feb. 27 e-mail to those appointees, he recognized that some might be unwilling to abide by the ethics pledge.
"While Secretary Gates continues to encourage you to stay if possible, it is also understood that the post-government employment restrictions imposed by the executive order may result in a reassessment of your decision," Rangel wrote. "Whatever your decision, your willingness to serve and contribute to the continuity of the operation of the department will be honored and appreciated."
In his most recent e-mail, Rangel noted, "Individuals who decide to leave prior to April 30 will not be penalized by being placed in a disadvantaged position simply because they agreed to voluntarily stay beyond Jan. 20."
About 250 political appointees worked at the Pentagon as of December and many were asked to stay on past the inauguration. A Pentagon spokeswoman did not know immediately how many appointees have agreed to sign the pledge.
The pledge was required by a sweeping ethics executive order Obama signed as one of his first acts as president. Among the biggest changes are restrictions on the "revolving door" between government service and the private sector.
Internal guidance prepared by the Defense Department general counsel's office stated, "Once you leave federal service, if you were a senior official you may not communicate with, lobby back to, or represent another before your former DoD agency for two years."
The rule also applies to new political appointees who, for two years after taking a position in the Obama administration, will not be allowed to participate in any matter involving their former employer or clients. Similar restrictions apply to appointees who previously served as registered lobbyists. The pledge does not affect perfunctory or administrative duties, or social interactions with former employers or clients.
The agreement also states that with few exceptions, appointees cannot accept gifts from registered lobbyists or lobbying organizations for the duration of their government appointment.
Among those exempt from the pledge are career officials acting temporarily in the absence of an appointee to a noncareer position, those designated as special government employees, uniformed service commissioned officers, and certain Schedule C appointees who have no policymaking role and have been properly exempted from filing a public financial disclosure report, the guidance said.
The general counsel's office can waive any of the pledge restrictions. But, the guidance stated that "waivers will be granted sparingly with as limited a scope as possible."
Megan Scully of CongressDaily contributed to this report.