City officials touted a record-low September crime rate on Tuesday, with decreases in every major category except one — rape.

There were 117 rapes reported in September 2017 compared with 113 in September 2016. That is an increase of 3.5%. Rape cases so far this year compared to the same period in 2016 are down 6 percent.

“Many of [the suspects] are known to [the victim],” NYPD Chief Dermot Shea said at a press conference in Manhattan. “So it’s not a case of finding out who did it.”

He said the NYPD breaks down rapes into three categories: domestic, not domestic but known to the victim, and stranger rapes.

He said rape cases where the victim knows the attacker are more difficult to win in court.

“The sexual offenses continue to be a challenge,” Shea said. “But I’m confident that everything we can do we are doing.”

The city saw a record low number of other index crimes for September 2017, as for every month so far this year.

There were 15 fewer murders reported in September, or a 42.9 percent drop, and 30 fewer shooting incidents, for a 27.8 percent decrease.

Overall, there were 458 fewer “index,” or major, crimes, for a 5.3 percent decrease in September 2017 compared with September 2016, according to an NYPD press release.

For the year to date, there have been 4,518 fewer reported citywide index crimes, or 5.9 percent less, compared with 2016.

“What we are seeing more and more is that we can no longer assume that there is any part of this city we can’t turn around,” Mayor de Blasio said.

“We are the safest big city in America and I’m telling you now we will get safer.”