Rahat and his 16-member troupe was detained at Delhi's Indira Gandhi International Airport Feb 13 for carrying $142,000 in cash and cheques when they were going to catch a flight to Dubai for their onward journey to Karachi.
After undergoing thorough investigation for almost a week, the singer and his manager were fined Rs.1.5 million ($33,000) each by Indian authorities to have their passports and other documents returned.
"It has been a tough week for me but I want to thank you for standing by me during this time," he reportedly told Malik over the phone.
He also lauded the efforts of Pakistan's High Commissioner to India Shahid Malik during his detention.
"I'll return to Pakistan anytime tomorrow (Monday)," he informed the minister.
The singer is expected to reaching Pakistan at 2 a.m. via Dubai.
In another development, Pakistani actress Atiqa Odho addressed a press conference in Karachi Sunday and called for "making a proper mechanism between India and Pakistan for facilitating the payments of artists working on both sides of the border".
"I have been writing to the government for the last three years but there has been no response," she said, adding: "The governments in India and Pakistan always wait for a disaster to happen before starting damage control."
"Rahat has committed a mistake and has also been a victim of the system," she said while calling for "support for the singer at this crucial stage".
"We must ensure that such a talented voice is not lost anywhere," she argued.
Several Pakistani artists have been appearing in Indian cinema and television programmes while the singers from the country have particularly been a rage in India.
Rahat Fateh Ali Khan and Shafqat Amanat Ali Khan have given Indian cinema several hit songs over the last few years.
Rahat was awarded the best singer award at the recent Filmfare awards function held in India for his song "Dil to bacha hai jee".
With the cultural and showbusiness activities in Pakistan shrinking because of terrorist activities, the country's artists have found a bigger platform in India to showcase their talent.