When employes of the embattled National Consumer Cooperative Bank came to work yesterday morning, they were told they would not be getting their paychecks, that the Treasury Department was holding the payroll hostage in a dispute over $60 million in NCCB funds.

By the end of the day, the employes had their paychecks but not before bank officials and members of Congress accused the administration of harassing the tiny bank that President Reagan wants to kill.

Treasury Department officials say they merely were being understandably careful in checking that the payroll request was legitimate, in light of what they consider the "improper withdrawal" by the bank of $60 million from the Treasury last month.

The central issue is whether the administration can impound the $60 million, funds appropriated by Congress for the Treasury to purchase NCCB stock in the last half of fiscal 1981. The cooperative bank is a quasi-government institution created by Congress and initially funded through the Treasury purchase of stock, to provide financing for consumer cooperatives.

The administration wants to close the bank by September and in the meantime has tried to impound its funds.

NCCB officials, buttressed by a ruling of the General Accounting Office, say the money cannot be withheld unless Congress approves the impoundment. Congress has 45 days to act on impoundment requests, giving it until Monday on the NCCB money.

Taking matters into her own hands, NCCB President Carol Greenwald last month simply sent over disbursement vouchers for the $60 million to Treasury, and they were honored. Treasury says it made a mistake in honoring the vouchers and wants Greenwald to give the money back. She has refused, pending congressional action.

The 15-member NCCB board, of which seven members were appointed by Reagan on Wednesday, also is to meet on Monday to discuss the bank's future. The board has the authority to give the money back.

Greenwald said yesterday the payroll holdup was done in retribution for her action and was a blatant attempt at "harrassment." She said bank officials were told by Treasury officials the funds were being held in "partial payment" of the $60 million, and that only expressions of congressional outrage freed the funds.

Jordon Luke, Treasury assistant general counsel for enforcement and operation, the senior Treasury official involved in yesterday's episode, said this is "absolutely false." A hold was put on all disbursements to the NCCB so their validity could be checked, he said.

He also said that the legitimacy of the payroll funds was not in dispute but that it required a meeting with about 10 officials from the Office of Management and Budget and the Departments of Treasury and Justice to make the decision to release the payroll funds.

Other decisions on how next to go about getting the money back were made at that meeting, but Luke declined to say what they were.