Akshay, who landed at the Chandigarh international airport on a chartered flight from Mumbai earlier in the day, drove straight to the high-security state police headquarters in Sector 9 here and appeared for the questioning.
He remained inside the headquarters for almost two hours.
When the questioning ended, Akshay was taken away in his vehicle through a side gate of the police premise to help him avoid the waiting media.
The SIT grilled Akshay regarding the alleged deal, his relationship with the sect leader and Badal. He was also asked if the Dera leader lived in the same locality in Mumbai as his, police sources said.
Akshay apparently challenged the SIT officials to show evidence of the allegations raised against him and not go only by hearsay, an officer not willing to be identified revealed.
Dismissing all allegations, the 51-year-old actor said that he had great regard for the Sikh religion and would never do anything to dishonour or hurt it.
Earlier, while coming out of the Chandigarh airport, he told the media in Punjabi: "Tussi vi aao, naal challo" (You too, come along). Before he raced pass in a luxury SUV.
The Punjab Police SIT, which is probing sacrilege of the Sikh holy book the Guru Granth Sahib and subsequent firing on protesters in 2015, had earlier in November summoned the "Gold" actor as a witness.
Akshay had on Tuesday moved a request that he be allowed to meet the SIT officials in Chandigarh instead of Amritsar, where he had been originally asked to appear.
He was questioned regarding his alleged role in brokering a Rs 100-crore deal between the Dera chief, who was later convicted of rape and sentenced to 20 years in prison and Badal in Mumbai in 2015 just days before the release of a film of Gurmeet Ram Rahim.
Akshay has denied the allegations, terming them to be "rumours and false statements".
"I have never ever met Gurmeet Ram Rahim Singh in my life, anywhere. I learnt from social media at some point that Gurmeet Ram Rahim Singh resided for a while at some place in my locality Juhu in Mumbai but we never ever crossed each other's path," Akshay had tweeted after he was summoned by the Punjab Police.
On his part, Sukhbir Badal said on Tuesday: "I have never met Akshay Kumar outside Punjab." Badal was questioned by the SIT here at the police headquarters on Monday.
He termed the questioning as a sham and alleged that the Congress government led by Chief Minister Amarinder Singh was indulging in "political vendetta".
Former Punjab Chief Minister Parkash Singh Badal was on November 16 questioned by the SIT headed by Additional Director General of Police Pramod Kumar and Inspector General Kunwar Vijay Pratap.
The senior Badal said that he told the SIT that he had not ordered firing on Sikh protesters agitating against the sacrilege incidents in October 2015.
Amarinder Singh had earlier said that his government had no role in the summoning of the Badals and the actor by the SIT.
The SIT was set up by the Amarinder government in September to probe the sacrilege cases and the firing ordered on those protesting the sacrilege in October 2015 when the Akali Dal-BJP alliance government headed by Parkash Singh Badal was in power in the state.
Two persons were killed in the police firing in Behbal Kalan village near Kotkapura town in Faridkot district.