Prince George's County officials are investigating the possible misuse of $110,000 in federal funds by operators of Assisi House, a nonprofit shelter for battered women.

A recent examination of the Upper Marlboro shelter's financial records revealed that Assisi operators had failed to return employe withholding taxes to the government, had not provided many of the social services promised, and could not account for money collected and used.

Assisi, the county's only home for battered women, receives most of its funds from the Comprehensive Employment Training Act (CETA), a federal manpower program administered by the county. It also receives private donations and got $15,000 from the Eugene and Agnes Meyer Foundation and the Redskins Foundation.

Since its opening 21 months ago, Assisi has been run by Elizabeth Fischer, who left her home in North Carolina as a battered wife and came to Washington, where she worked for a short time at the House of Ruth, the city's shelter for battered women.

Eugene T. Lauer, the deputy county administrative officer, said yesterday that in the course of a routine examination, the county found "a number of deficiencies that caused some problems." As a result, the county government, which oversees all CETA programs in Prince George's called in an independent auditor to examine the Assisi books and halted all payments to the shelter until the investigation is completed.

William E. Knight, vice chairman of Assisi's board of directors, said yesterday he is certain that Fischer will be able to account for the CETA money.

"Everything is in place," Knight said. "Maybe Column A is not added properly or Column B entered properly. But everything is there. It is just a matter of getting it organized."

Fischer said in an interview yesterday that her group "is having growing pains. We're going from a volunteer organization to a funded organization. We've been playing catch up with the books."

Assisi is also being investigated by the county's Commission for Women as a result of complaints by employes of the shelter that Assisi is not being operated properly and does not offer many of the services that Fischer said it does.

The center, located on 68 acres of rolling countryside on the former site of the German Orphans' Home, boasts 11 auxiliary shelters, a 24-hour hotline, and counseling and therapy for children of battered women as well as for abusers.

The employes, who testified secretly before members of the commission, have also alleged that some of the Assisi funds may have been improperly used and that Fischer threatened them when they questioned her policies, according to sources.

Susan Helfrich, executive director of the commission, would not comment yesterday on the Assisi inquiry.

However, one source familiar with the investigation said, "The problem is that moneys have been coming in and moneys going out as petty cash, and nobody knows what it was spent for."

The investigations by the commission and independent auditors have sparked enormous controversy on Assisi's board of directors, which includes some of the county's most prominent politicians and community leaders, including County Council members and state legislators.

This week a board meeting became heated when some members charged that Fischer and the shelter were being unfairly attacked. Other board members have said privately that they were concerned about the allegations of financial mismanagement and hoped that the county audit would help to eliminate any problem that might exist at the shelter.

According to several internal reports conducted by the county's CETA monitors over the last few months, Assisi had failed to maintain complete records of deposits, withdrawals and transfers of money.

The reports also found that Assisi had improperly mixed CETA funds and financial records with other funds and therefore may have used the federal money for inappropriate purposes.

In Addition, the reports found, Assisi has failed to pay several thousand dollars in payroll taxes to either the federal or state governments, despite having withheld money to pay those taxes from employe paychecks.

Because of these problems, which the report said amount to "inexcusable and unsound business practises," the CETA monitors recommended that the county "re-evaluate (Assisi's) capabilities for administering a CETA program."

Fischer said yesterday that without the CETA funds the shelter would have a difficult time continuing in operation.