The Long Island mother of Kansas City Chiefs football player Jovan Belcher told investigators her son argued with his girlfriend Kasandra Perkins over their baby’s paternity before he shot her dead and killed himself, The Post has learned.

Cheryl Shepherd — who was in her son’s suburban Missouri home the morning he shot Perkins nine times — told investigators after the shootings that there were questions about whether the West Babylon, LI-raised linebacker was the father of the couple’s 3-month-old daughter, Zoey, said sources familiar with the situation.

“The mother believed that there was an issue over whether [Belcher] was the father,” said a source close to the Chiefs with knowledge of the situation.

“She said he [believed he] wasn’t necessarily the father of the child.”

A Kansas City law-enforcement source confirmed, “She told [police] there was a question about the paternity.”

It’s unclear if the paternity issue was the reason for the final, violent end of the troubled relationship between Belcher, 25, and Perkins, 22.

“But the implication was that [paternity] was what the two of them were fighting about — that the baby might not have been his,” a source said.

Belcher fatally shot Perkins at 7:50 a.m. Dec. 1 after a heated argument that started at 7 a.m. Shepherd, who had been visiting the couple, called 911 after her son fled the bloody scene. Before bolting, Belcher apologized and kissed the dying Perkins and their baby daughter good-bye, according to the Kansas City Star.