A manhunt is underway for a Long Island dad who police believe fled the state with his 2-year-old son and a rifle — and possibly set his own home on fire before doing so, authorities and relatives said early Wednesday.

Jovani Ligurgo’s mother dropped him off with his father, John Ligurgo III, on Tuesday at 7 a.m. at the man’s Coram home.

When the 43-year-old father did not show up with the tot at the pre-arranged meeting time of 3:30 to 4 p.m., the concerned mother called 911, according to Suffolk County police.

Meanwhile, officers were called to a report of a fire at 3:35 p.m. at the man’s Bretton Woods Drive home — but the house was empty. No note was found, and Jovani’s belongings appeared to still be at the home, the boy’s adult brother, Anthony Busone, said in a message to the Post.

Police are investigating whether the blaze was set intentionally.

“[T]here has not been a definitive answer on if it was intentional, but my personal opinion is that he did it on purpose,” Busone, 26, said.

Busone alluded to an ongoing custody battle between his mother, Maria, and John, which started about a month ago.

“I wouldn’t put anything past him at this point,” he noted.

The last time Maria spoke to John was when she dropped Jovani off with him on Tuesday morning, Busone said.

John is believed to have run off with his son in a black Jeep Grand Cherokee with New York license place GAV4699. Police warned he might be armed.

Detectives are asking anyone with information to call 631-854-8652.