The militants of the Balochistan Liberation Army targeted the Quaid-e-Azam Residency in Ziarat, a holiday resort located about 120 km from the provincial capital of Quetta, at 1:15 AM.
They planted and set off five bombs and then opened fire. The explosions and gunfire triggered a blaze that was extinguished after four hours. A policeman was killed in the shooting, officials said.
In a report presented in the National Assembly or lower house of parliament, Interior Minister Chaudhry Nisar Ali Khan said the Residency was attacked by about five militants, who removed a Pakistani flag and raised the flag of the Balochistan Liberation Army in its place.
The wooden parts of the building, furniture and memorabilia associated with Jinnah were destroyed by the blaze.
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Footage on television showed that the roof of the building had collapsed and only its structure made of bricks was left intact.
District police chief Asghar Ali said a bomb disposal squad had found and defused six more bombs, each containing about three kilograms of explosives.
He said it took longer than expected for the fire to be controlled as there are no fire tenders in Ziarat.
A fire tender sent from Quetta was used to put out the blaze.
The Residency, built in 1892, was originally used as the summer residence of the Agent of the British Governor General.
Jinnah spent the last days of his life in the building while suffering from tuberculosis and the structure was later declared a national monument.