V.D. Pandya made the accusation on Friday when he testified before a federal commission probing last year's Hindu-Muslim riots that left around 2,000 people dead.
Pandya said the state's Bharatiya Janata party, BJP government headed by Chief Minister Narendra Modi had arranged the killing.
"Modi wants to defame Haren's name because of selfish political reasons. He wants to prove that Muslims have killed him but it is far from truth. Modi is the motivator of the intentional political murder of Haren," Pandya said in a statement to the commission.
Congress, the main opposition party in Gujarat, has also accused Modi of involvement in the killing.
The government has denied the allegations.
Pandya's son, Haren, who was the province's home minister and a BJP member, was shot dead on 26 March in the state's capital Ahmedabad.
Several witnesses have named him as the instigator of the riots.
The federal commission has received 4,500 submissions from riot victims around Gujarat.
Another contentious issue that led to sectarian violence - the Babri mosque row in Ayodhya will top the agenda of India's ruling Hindu nationalist BJP meeting.
The Babri mosque's destruction
That national executive meeting in the central Indian town of Raipur is the first time since 1989 that the party discusses the issue.
The dispute centres around the ruins of the 16th century Babri mosque which was demolished by thousands of hardline Hindus in 1992 in a campaign led by the BJP.
The destruction led to some of the worse nationwide Hindu-Muslim riots.
The Hindus believe the mosque was built on top of a shrine at the birthplace of their god Ram and they have since been pressing for the "reconstruction" of the temple.
In preliminary findings released in June the Archaeological Survey of India said it had found no evidence from a dig at the site that it ever held a Hindu temple.
BJP sources said the meeting may pass a resolution that would reaffirm the party's commitment to building the temple and at the same time would call for talks to continue between the two communities to find a mutually acceptable solution.