A Manhattan mom was taken into police custody after she reported one of her children missing in Manhattan Wednesday morning and then refused to let police into her home, where another child had been left alone, an NYPD spokesman said.

The woman initially told police her 4-year-old child went missing in the subway at East 59th Street and Lexington Avenue around 8:30 a.m.

“’I have lost touch with my 4-year-old,’” she told cops, according to an NYPD spokesman. “‘She was with me, and she’s no longer here.’”

But when police drove the mother back to her home in Harlem, she became emotionally unhinged and refused to let them inside, the spokesman said.

“’No, you’re not going in,’” the mother told them.

Cops then heard a voice behind the door.

At that point, “they take the door” and discover a 12-year-old inside alone, the spokesman said.

The younger child was later located at a nearby daycare, safe and sound.

Charges against the mother were pending.