Shafqat Jalil said the government “absolutely disassociated” itself from comments by Railways Minister Ghulam Ahmad Bilour.
Innocence of Muslims, produced in the US, has led to a wave of protests in the Muslim world and many deaths.
The bounty offer came a day after at least 20 died in clashes in Pakistan.
Friday’s violence, which saw protesters pitted against armed police, occurred in cities throughout Pakistan, with Karachi and Peshawar among the worst hit.
“I will pay whoever kills the makers of this video $100,000,” the minister said.
“If someone else makes other similar blasphemous material in the future, I will also pay his killers $100,000.
“I call upon these countries and say: Yes, freedom of expression is there, but you should make laws regarding people insulting our Prophet. And if you don’t, then the future will be extremely dangerous.”
At one point, he even called for the help of the Taliban and al-Qaeda in killing the filmmaker.
His ANP party, which is part of the governing coalition, said this was a personal statement, not party policy, but added that it would not be taking any action against him.
Shafqat Jalil said: “He is not a member of the [ruling] PPP [Pakistan People’s Party], he is an ANP politician and therefore the prime minister will speak to the head of the ANP to decide the next step. They are not ruling out action against him but say he will stay in his post for now.”
Meanwhile, scores of people were reported to have been injured on Saturday in a clash in Bangladesh’s capital Dhaka between police and hundreds of demonstrators.
Police fired tear gas and used batons to disperse stone-throwing protesters who set several vehicles alight, the Associated Press news agency reports.
In Pakistan itself, a peaceful demonstration was held in Islamabad. Protesters marched through the capital and gathered near parliament, chanting slogans against the filmmaker and demanding his punishment.
And in Nigeria, tens of thousands of Muslims marched in the northern city of Kano in a protest that passed off peacefully.
Marchers shouted “death to America, death to Israel and death to the enemies of Islam” in a procession several kilometres long. US and Israeli flags were dragged through the dirt.
The exact origins of Innocence of Muslims, the low-budget film that has prompted the unrest, are unclear.
The alleged producer of the trailer of the film, Nakoula Basseley Nakoula, is in hiding.
Anti-US sentiment grew after a trailer for the film dubbed into Arabic was released on YouTube earlier this month.
US citizens have been urged not to travel to Pakistan, and the US embassy has paid for adverts on Pakistani TV showing President Barack Obama and Secretary of State Hillary Clinton condemning the film.
Although US targets have borne the brunt of protests against the film, anti-Western sentiment has been stoked further by caricatures of the Prophet Muhammad published this week in the satirical French magazine, Charlie Hebdo.
France shut embassies and other missions in about 20 countries across the Muslim world on Friday.
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