Ali Raza, also a doctor, alleged that his wife Mehwish Noor threw their son Danish from the rooftop after a quarrel with him yesterday.
He said the boy was killed instantly.
Raza, a resident of Sabzazar in Lahore, told police that his wife had developed some psychological disorder.
Police arrested Noor and registered a murder case against her on the basis of a complaint filed by her husband.
Police officials said Raza had married Noor about two years ago.
On Sunday night, Noor had called a police helpline and claimed that her husband wanted to go to Britain without her.
She further said she feared that his parents would kill her in his absence.
Police officials said they were investigating Noor's claims.