Chief Justice Warren E. Burger yesterday disputed complaints that the Supreme Court has been closing the doors of federal courthouses to minorities, the poor, advocates of unpopular causes and victims of government misconduct.

Burger referred to the complaints in his annual speech to th American Law Institute, a group of leading lawyers, judges and legal educators that meets here each spring to seek improvements in the law.

Burger said that civil suits filed in the 94 U.S. Distirct Courts increased from 77,000 in 1969 to 130,000 in 1976.

Saying that the nature of the filings "is more important than the old number," he cited the increase in claims under the Social Security Act - from an average of five per court per year in 1969 to more than 100 in 1976. During the same time period, civil rights cases multiplied tenfold.

Going back to 1960, Burger recalled that the number of filings by prisoners seeking relief in federal courts was only 2,000 - compared with 19,000 last year.

The Chief Justice then turned to an analysis of the Supreme Court's full, signed opinions, which in the eight years since he joined the court have averaged 122 annually. The average for the period 1961 through 1968 was 100, and for the years 1953 through 1960 it was 90.

Cases decided from 1969 through 1976 included 75 dealing with the rights of racial minorities and 24 indian claims cases, Burger said. He gave this further listing.

Forty-one dealt with the rights of prisoners, probationers and parolees; 27 with the rights of welfare recipients; 25 with press rights; 21 with women's rights; 15 with the right to counsel, 11 with the rights of illegitimate children, 10 with students' right, six with the rights of non-tenured employees, and five with mental patients and mental institutions.

Following custom, Burger adhered closely to his prepared text and did not take questions. He also did not identify the "voices . . . raised from time to time complaining that the federal courts are closing their doors . . ."

But strong criticism has come from, among others, Sen. Charles McC. Mathias Jr. (R-Md.) and Gaylor Nelson (D-Wis.), the American Civil Liberties Union and the Society of American Law Teachers.

No Criticism, however, has been more forcefull than that in the court, particularly in dissents by Justices William J. Brennan Jr. and Thurgood Marshall.

Last March, for example, Brennan, joined by Marshall, accused the majority - including Burger - of requiring a U.S. District Court in a case involving debtors "to eject the federal plaintiff from the federal courthouse," which "effectively cripples the congressional scheme" enacted more than a century ago.

Brennan went on to attack the majority for a series of decisions that "increasingly . . . bar the federal courthouse door to litigants with substantial federal claims." He emphasized rulings that "weaken drastically the federal courts' ability to safeguard individuals from unconstitutional imprisonment" and that condone "both isolated . . . and systematic violations of civil liberties."