The D.C. City Council passed emergency legislation yesterday giving 90 days' grace to more than 100 nonprofit organizations, including some of the best-known churches and schools in the city, that have been delinquent in filing tax forms and face thousands of dollars in penalties.

Council members complained that these tax-exempt organizations appear to be ignoring the law but acknowledged that the institutions are too important to the city or have too much political clout to be heavily penalized.

The organizations were listed as the National Shrine of the Immaculate Conception, the Washington Hebrew Congregation, All Souls Church of Washington, National Childrens' Center, Sisters of the Visitation, Goodwill Industries, the Florida Avenue Baptist Church and Howard University Hospital.

"I have no disagreement with the legislation ," said council member John Wilson (D-Ward 2), chairman of the Finance and Revenue Committee. "What bothers me is that we make laws, we change the laws and nobody pays attention to the laws we make."

Council member H.R. Crawford (D-Ward 7), the sponsor of the emergency measure, said that without a reprieve, properties owned by the organizations soon would be advertised to be sold for taxes -- although the possibility of the city placing any of those properties on the auction block is highly remote.

"The city is not going to sell the Shrine of the Immaculate Conception," Wilson said.

Council member Betty Ann Kane (D-At Large) complained that the law "is a big gift from the city."

"Some of them are very big organizations with very large staffs, and I am not sure why they have missed the deadline and filed late," Kane said.

The law was approved by a unanimous voice vote.

Under the old law, which the emergency legislation replaces for 90 days, organizations are required to file by March 1 a form specifying the use of a piece of property. If they fail to file on time, the old law empowers the city to penalize the organization an amount equal to at least 30 days' worth of property tax. The amount of the penalty rises, at the discretion of the mayor, to the total number of days the organization is delinquent.

The emergency legislation changes the penalty to $100 a day, regardless of the property assessment, and permits the mayor to waive the penalty during the 90 days. The beginning of the period affected by the law is March 1, 1983, the first year of the law.

About 1,900 tax-exempt groups in the District are required to file the annual use report. Crawford defended some of the delinquencies by saying that many organizations did not understand the law.