For Karen Diehlman, a fourth grader at Archbishop Neale School in La Plata, Md., math and reading are difficult subjects. Until this year, special public school teachers tutored her in the Catholic school as part of a program paid for by the federal government.

But since the Supreme Court ruled in July that public funds may not be used to pay for instruction in religious schools, Washington area public school administrators have been scrambling to find alternative sites, often involving busing, to offer Diehlman and nearly 3,000 other parochial students remedial aid that they are entitled to under the federal government's program for educationally disadvantaged children, known as Chapter 1 funding.

The issue has become especially volatile in Charles County, where parents of nearly 90 of the 108 children eligible for the remedial aid have refused to bus their children to public schools.

They complain that the decision discriminates against Catholic taxpayers and forces their children to miss at least three hours a week of other essential academic subjects.

Angie Diehlman, along with 40 other parents at Charles County's Archbishop Neale, has decided not to bus Karen to a nearby public school site.

"Why should I do that and risk her falling behind in the other academic subjects she'll be missing?" Diehlman said. "She's having a lot of trouble right now . . . . It's a mess, a real mess. I work with her a lot at home, but she's not getting the same kind of reinforcement at school as before," Diehlman said.

The Supreme Court's ruling July 1 struck down New York City's use of federal remedial education funds for teachers in church-related schools and the use of state funds in Grand Rapids, Mich., for teaching remedial and enrichment courses in parochial schools.

That decision disappointed the Reagan administration, which supported the funding and which supports measures to allow prayer in school.

The changes hit hardest at Catholic schools, which made up about 85 percent of the Chapter 1 programs nationwide and were the only religious schools in the local area that participated.

After weeks of frantic midsummer planning, Maryland public school administrators say the 2,735 children from 56 Catholic schools that are eligible for the remedial program are now either walking to libraries and other public buildings in densely populated neighborhoods or being provided bus transportation to neutral sites in rural counties.

In the District of Columbia, between 350 and 400 students from eight Catholic schools are walking to nearby public schools for the program, said Anne W. Pitts, executive director for Chapter 1 funding in the District.

In Virginia, the supplemental tutoring program is on hold as a result of the Supreme Court ruling for about 100 children at eight Arlington, Fairfax and Alexandria Catholic schools while officials wrestle with the legality of hiring a third party to provide the remedial aid, said Marie A. Powell, assistant superintendent of Catholic schools.

"It's been a logistical nightmare," said Jerome R. Porath, superintendent of schools for the Archdiocese of Washington, which includes the District and Prince George's, Montgomery, Charles, Calvert and St. Mary's counties in Maryland.

"I don't know of anyone who thinks this is a good decision," he added. ". . . It will cost more money and not deliver the same quality of services. The only children being penalized are the disadvantaged ones."

Chapter 1, which until recently was known as Title 1, came into being as a cornerstone of President Johnson's Great Society legislation of the mid-1960s. It was designed to supplement the education of disadvantaged elementary school children.

Before the Supreme Court's decision, Porath said, "teachers have always been able to go into parochial classrooms and work with children without pulling them out of class."

Supporters of the Supreme Court ruling argue that they are not opposed to children in religious schools receiving remedial aid but insist that it was necessary to maintain the constitutional separation of church and state.

"The Supreme Court found that using federal money in a parochial school was unconstitutional because it created too much of an entanglement between the operation of the government program and the religious activity," said Arthur B. Spitzer, legal director for the American Civil Liberties Union's local chapter.

The ACLU has no objections to children getting the remedial help "as long as it is given in a neutral public facility free from religious overtones," Spitzer said.

Officials have expressed concerns that the changes will steeply increase the cost of the program. In Prince George's County, for example, transportation for the 211 participating parochial children is expected to add $20,000 to the cost of the remedial program, according to Chapter 1 coordinator Yvonne Brown.

In Charles County, officials said they are exploring the possibility of contracting the services to educational consultants who would service the parochial schools from mobile vans.

In the District, however, the changes in the Chapter 1 program have caused less confusion. "The decision has created chaos across the country, but in the District we're very fortunate because our private schools are within two or three blocks of the neutral public school site," said Pitts.