The Pakistan Cricket Board (PCB) said in a statement on Monday that it had "requested the Board of Control for Cricket in India (BCCI) to change the second Test venue of Ahmedabad on the grounds of security".
India last month proposed the major western city -- where at least 2,000 people were killed in bloody Muslim-Hindu religious violence in 2002 -- as one of the Test venues for the tour starting later this month.
Pakistan is predominantly Muslim, as were those who died at Ahmedabad, while India is majority Hindu.
However, the PCB denied media reports that the decision was politically motivated.
"We decided to request the change only after receiving a report from our venue assessment committee, which recently toured India," said PCB spokesman Abbas Zaidi.
Pakistan are due to play three Tests and five one-day games as well as two side matches on their first full tour of India in six years. They played a commemorative one-day match in India last year.
"In making the request the PCB wishes to preserve and strengthen the bilateral relations that have been enhanced at the public and government level after the resumption of ties between the two countries," said Zaidi.
The governments of nuclear-armed rivals India and Pakistan are engaged in a tentative, year-long peace process that has seen increased political, social and cultural contacts.
"The PCB contradicts reports suggesting any motive other than security -- such as people saying it may be political or anything -- in making this request for change and maintains that the venue issue should be amicably resolved," said Zaidi.
Mohali, in north India, and the southern metropolis of Bangalore are the other two proposed Test venues.
Pakistan was expected to reject Ahmedabad after Pakistan's foreign ministry and ministry of sports and culture also raised concerns. Madras is the likely replacement if the Indian cricket authorities accept the request.
The proposed venues for the five one-dayers are Kochi, Visakhapatnam, Kanpur, Jamshedpur and New Delhi.
Pakistan last toured India in 1999 despite threats from Hindu fundamentalists who also dug up a pitch at the Feroze Shah Kotal ground in New Delhi.
Pakistan will return from Australia on Tuesday and after a short training camp in Lahore will fly to India on February 25.