The case has attracted attention, not only in Pakistan but also from other countries after reports suggested he was falsely implicated in the drug case.
"While respecting the judicial system of Indonesia, the Government of Pakistan hopes the clemency appeal filed by Ali will be considered favourably by the Government of Indonesia on humanitarian grounds," said a statement issued by the Foreign Office.
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According to the Foreign Office, Ali was arrested on drug trafficking charges from Bogor, Indonesia in November 2004. The district court awarded him a death sentence in 2005, and the higher court upheld the district court's decision in 2006.
The charges were framed against Ali on the basis of a statement given by a single witness, who was himself sentenced to death.
He filed two appeals for judicial review, first in 2008 and again in 2013, but both were turned down. The last legal course available is seeking clemency which he has now applied for.
The Foreign Office said Pakistan was taking up the issue with the Indonesian government at various levels, through both political and diplomatic channels, ever since his arrest in 2004.
"The matter was taken up at the level of the heads of state in 2007. The Indonesian side has been repeatedly urged to review the case of Zulfiqar Ali."
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Most recently, Adviser to the Prime Minister on Foreign Affairs Sartaj Aziz raised the matter with the Indonesian ambassador. This was followed up by the additional secretary (Asia-Pacific) with the Indonesian ambassador.
Even the Pakistan Embassy in Jakarta was directed to take up Ali's case, with the Indonesian authorities at all levels and with all institutions concerned.
The Embassy has also maintained contact with Ali through consular access, the Foreign Office said, adding it has been in regular touch with his family, his lawyer and others concerned. It also hired a lawyer to pursue his case in court.
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