Three years after the city launched an investigation into whether certain ultra-Orthodox Jewish schools were providing an adequate education in secular subjects, it revealed on Thursday that it had made little progress. In a letter to the state’s Education Department seeking guidance, Richard A. Carranza, New York City schools chancellor, acknowledged that investigators had managed to visit only half the schools involved.

The inquiry began in the summer of 2015, when a group of parents, former students and former teachers at yeshivas told the city that 39 schools were not sufficiently teaching subjects, like math, science, and English, leaving students ill-prepared for adulthood. The Education Department then launched an investigation of 30 of the schools, after determining the others were either no longer operating or did not fall under its jurisdiction.

As part of its investigation, the Education Department interviewed some of the parents and students who brought the complaint, who had experience at 11 schools. Most of those interviewed said the boys schools taught math and English for at most 90 minutes a day until boys turned 13, at which point secular instruction stopped. Some said attendance during secular instruction was voluntary. And while occasional science experiments might be done in class, they said there was no science curriculum. New York state law requires that nonpublic schools provide an education that is “substantially equivalent” to that of public schools.

Education officials also made announced visits to the schools, but, they said, 15 yeshivas did not allow them inside. “The D.O.E. has made repeated attempts to gain access to the schools,” Mr. Carranza said in the letter. “The long delay in scheduling visits to this group of 15 schools is a serious concern.”