Another civil rights "misunderstanding" has sprung up around the Reagan administration this week, this one not involving the tax-exempt status of schools that practice racial discrimination, but instead the president's plans for the Equal Employment Opportunity Commission.

The misunderstanding arose out of a speech by the EEOC's new general counsel, Michael Connolly, formerly an attorney for General Motors in Detroit, to a group of EEOC attorneys and employes called to Washington from all over the country for a meeting Jan. 13.

A number of the lawyers who attended say that Connolly informed them he planned to change policy in a number of areas. The changes included:

* Narrowing the scope of action in sexual harassment cases to make employers liable only in cases where management is accused of sexual harassment. Under current guidelines, an employer can be held responsible for sexual harassment by any employe as long as the problem has been brought to the employer's attention.

* Discouraging age discrimination lawsuits in cases where they would provide a severe "economic hardship" to the employer.

* Shifting emphasis away from class action lawsuits and toward individual lawsuits, especially in cases where employers have made an effort to address the complaints.

* Ending the pursuit of complaints in which workers claimed they were denied equal pay for comparable work. "He told us he was a believer in the marketplace and that we would no longer pursue those cases," said one lawyer.

Several attorneys present say that Connolly told them "there was an election in November 1980 and things are going to change around here."

Connolly said yesterday that the controversy over his speech was the result of a "misunderstanding" and that he was talking about his own "philosophies," not actual policy changes.

"I do not forsee any major changes" in policy, he said. "The commissioners and chairman vote on policy changes . . . . I think maybe they the lawyers may have misunderstood where I was coming from."

But persons present at the meeting say Connolly was talking about policy changes. "Connolly took it upon himself to tell the field people what the commissions policies should be," said one employe. "He was telling them, don't bring me these types of cases. Don't bring me this. Don't bring me that."

EEOC lawyers as well as groups that deal with the commission say that even if Connolly was only expressing his own philosophies, they are afraid he could affect policy through his authority to make the final decision on which cases go forward into litigation.

Arkie Byrd of the Women's Legal Defense Fund yesterday called Connolly's comments an example of the administration's retrenchment in EEO enforcement and civil rights in general.

"The general counsel has never had this authority legally. To assume he can just usurp responsibility of the commissioners is more than arrogant. It's rank stupidity," she said.

One EEOC lawyer said Connolly has already decided not to pursue several cases similar to others that are currently before the courts. Connolly said that he has turned down four cases, but with legal justifications.

Following Connolly's statement, sources say, J. Clay Smith Jr., acting chairman of the EEOC and a Carter administration appointee, protested that it was up to the commissioners--not the general counsel--to determine commission policy. The sources say Smith told Connolly that employes who do not carry out commission policy are subject to disciplinary measures. Smith's appointment expires in July.

At this point, the five-member commission is made up of two Carter appointees (including Smith) and a commissioner appointed by Reagan Dec. 21; there are two vacancies. For nearly three months, from Oct. 1 to Dec. 21, there were only two commissioners, both Carter appointees and less than the three required for a quorum.

EEOC lawyers who talked about the meeting say they are afraid Connolly's statements reflect administration sentiments and that the changes could be put into effect when the president appoints the remaining commissioners.

"The changes could have major implications," said one lawyer. "He obviously wants to make it easier for employers who make some effort toward repenting. But he did not make it clear what would be considered an adequate effort at addressing the violation. It could be interpreted to be almost anything . . . .

"And he's saying that instead of pursuing broader aspects of discrimination by suing on a class basis, we should go after individual cases . . . . Obviously, what's going to happen is we will have a limited ability to bring the larger cases alleging race or sex or national origin discrimination," he said.

Connolly conceded that there will probably be fewer class-action suits than in the past, but he said that was largely because of budget considerations. "It's a question of using the resources we have to the best of our abilities," he said.