Delays filling senior jobs in the Carter administration have left some government agencies with a serious shortage of executives.

In many departments, unconfirmed appointees are performing policy-making roles, though without legal authority to fulfill their new duties formally. Many of these persons have been put on their agency payrolls as consultants or temporary employees.

President Carter said at his news conference yesterday that the administration has "only appointed now about two-thirds of the subcabinet members in the major departments," but in fact only a handful of subcabinet nominations have yet reached the Senate, which must confirm many of them.

Sources in a number of government agencies said this week that the absence of confirmed policymakers in senior positions has hampered government.

Several members of the new administration and senior civil servants said they thought the Carter team's desire to get off to a running start an effective, pre-inaugural transition has now been set back in many departments.

The process of selecting, clearing and formally nominating subcabinet officials has proven much more complicated than the Carter team had originally expected. A major source of delay has been the new admistration's insistence on unprecendented financial disclosure by those named to policymaking jobs.

The White House has decided not to nominated any appointee formally until he or she has worked out a plan for financial disclosure that satisfies the President lawyers. According to one well-placed source, this process has turned out ot be both painful and difficult for some appointees - particularly those with substantial private wealth.

Several White House officials have said during the past two weeks that the FBI and Internal Revenue Service were both sources of delay in the clearance process. Spokesmen for both agencies insist that they are clearing appointees steadily, meeting their own deadlines for doing so.

The Carter administration decided not to begin FBI checks on individuals until they were actually designated for specific jobs, a fact that delayed the initiation of FBI clearances in many cases.

An informal survey of government agencies revealed these consequences of the absence of subcabinet appointees:

The Enviornmental Protection Agency - where no new appointees have yet shown for work - will not testify at hearing this week on amendments to the Clean Air Act, the most controversial and significant piece of pending enviornmental legislation.

"We are to some degree impeded until Carter's selected administrator is in place," said John R. Quarles Jr., the acting EPA administrator and a holdover from the Ford administration. The EPA has not "come to a grinding halt," Quarles added, but said it did lack executive guidance.

At the Department of Housing and Urban Development, Secretary Patricia Roberts Harris is the only new appointee on the job. She held a new briefing last week to assure reporters that acting officials in every office were fulfilling the department's obligations while she assembles a management team.

According to Richard Hite, deputy assistant secretary of interior, the absence of new poilicymakers there may mean that hearings on the department's new budget will be "carried on without representation by the top policy people" on Secretary Cecil D. Andrus' staff.

"You need the top policymakers to get the machine in motion," Hite said.

At the State Department, only Secretary Cyprus R. Vance and Under Secretary Philip Habib, the No. 3 man, have been confirmed. Appointees have been chosen for every other major post, however, and these people are on the payroll as temporary employees, and are performing the tasks they will deal with once they are confirmed by the Senate.

Vance and Habib had planned to tour the Middle East together beginning next week, but Richard Moose, the new deputy under secretary for administration, said Habib would stay behind if Deputy Secretary Warren Christopher is not confirmed before the trip begins.

Christopher's nomination reached the Senate yesterday. If Vance and Habib had left the country together, a relatively junior official - a career Foreign Service officer now serving as an assistant secretary - would have been acting Secretary of State in their absence.

Because of the backlog clearances and confirmations, it appears unlikely that the new administration will be fully staffed before next month at the earliest.

No appointments have yet been announced to the regulatory commissions, or to the many vacant ambassadorships.