Jones, who has been named head coach of the Islamabad United team in the Pakistan Super League, landed at the Benazir Bhutto international airport in Islamabad last night only to be told that his Pakistani visa had expired.
"We found out that he didn't have a valid visa to enter Pakistan and we have deported him as per immigration laws," an official in the immigration department at the airport told PTI.
Last week the 54-year-old was hired as the head coach of Islamabad United in the Pakistan Super League (PSL).
Sources said Jones had tried to contact the Islamabad franchise owners and the Pakistan Cricket Board to help him resolve the visa issue but was told he did not have a valid visa.
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Jones is among a list of foreign coaches signed up by the PSL franchises for the tournament to be held in the UAE from February 4.
Jones has visited Pakistan in the past for commentary assignments and recently also appeared as an expert for the state owned television channel.
Jones arrived in Lahore from Dubai this evening, Geo News reported.
Meanwhile, the Interior Ministry ordered action against the foreign airlines which brought Jones to Islamabad from Dubai without a valid visa.
A statement from the ministry quoted Interior Minister Chaudhry Nisar as saying that action would be taken against all those foreign carriers which violate the immigration laws of Pakistan.
Nisar said the impression was wrong that the ministry could allow any foreign national to enter Pakistan without a valid visa.
On the cricketing front, the former Australian batsman is also facing resistance from some former Pakistan players who have questioned his appointment in the PSL pointing out he was suspected of fixing even by the Australian cricket authorities who then quietly sidelined him from the national team.