Police seized the cash from the vehicle at the Bagepally toll-gate near Hindupur town and arrested one person identified as Harishnanda Shetty. A trust official was believed to have given him the money.
A police officer said the arrested person would be taken to Puttaparthi for investigations.
The money was seized two days after the trust opened Yajur Mandir, the residential quarters of the Sai Baba at Prashanti Nilayam in Puttaparthi.
The trust on Friday declared that it found Rs.11.56 crore, 98 kg gold and gold jewellery and 307 kg of silver articles inside which had been deposited with the State Bank of India (SBI).
The arrest and recovery of money has strengthened the apprehensions of a section of devotees that huge amounts of cash and jewellery might have been shipped out of Yajur Mandir when Sai Baba was battling for life at a hospital. The spiritual guru passed away on April 24.
Some devotees claimed Yajur Mandir had hundreds of crores of cash, ornaments, diamonds and other articles gifted by his followers in India and abroad. According to them, most of the cash and other valuables were slipped out of Prashanti Nilayam when Baba was in hospital.
As the news of police seizing the cash spread, trust member and Sai Baba's nephew R.J. Ratnakar visited Yajur Mandir on Sunday morning. He was accompanied by another member S.V. Giri.
Meanwhile, police in Puttaparthi started checking of vehicles at exit points. Police reportedly seized two bags from a bus passenger but it was not immediately known if they contained cash.
Taking a serious note of the happenings, the Andhra Pradesh government said it would intervene if the trust was found not discharging its responsibilities.
Revenue Minister Raghuveera Reddy, who hails from Anantapur district, said action would be taken if anyone was found guilty.