The singer, who had directly landed here from Abu Dhabi to participate in a programme organised at a city-based hotel last night as part of the New Year eve celebrations, was sent back as Pakistani nationals are only allowed to enter the country through Delhi and Mumbai, according to officials.
Khan then took a flight to Delhi and came to Hyderabad for his performance.
The singer, 42, today faulted the airlines for the fiasco and said the authorities were only following the rules.
"He (Khan) landed here yesterday morning. But he was denied entry as he did not fulfill immigration rules. So he was sent back (to Abu Dhabi)", an immigration official told PTI.
Asked about the incident, Khan told PTI, "The authorities and I were right in our own ways and the airline in question was wrong as they should have known that as a Pakistani national which ports in India we are authorised to travel. Hence, it was their fault and I as an individual had to make this journey in 29 hours."
A senior official of an airlines said Pakistani nationals can enter India only through Delhi and Mumbai airports.
"Khan had to go back to Abu Dhabi and flew back to Delhi. From there he came to Hyderabad and performed at the event," Ena Sharma, an official associated with the event, said.
Meanwhile, a senior police official said the movements of all Pakistani nationals entering into the country are recorded at the entry points of New Delhi and Mumbai.
Since Hyderabad does not figure into the authorised entry points, Pakistani nationals are not allowed to enter the country through this airport, he added.
The immigration official said that Khan was deported back to UAE by the same UAE-based airlines.
Khan is very popular in India thanks to his Bollywood numbers such as 'Mann ki lagan', 'Jiya dhadak dhadak', 'Bol na halke halke' and 'Dagabaaz re'.