The Pakistan government on Saturday again issued detention orders for Zakiur-Rehman Lakhvi, the alleged mastermind of the Mumbai attack, a media report said.
The Islamabad High Court on Friday ordered his release after declaring his detention illegal, Khyber News reported.
The Islamabad deputy commissioner had also issued his release order.
India had strongly reacted to the court order and summoned Pakistan high commissioner to India to lodge a protest.
Similarly, the Pakistan foreign office also summoned the Indian high commissioner to lodge a protest over the delay in the Samjhauta Express case.
The Pakistani government had taken Lakhvi and six other suspects into custody in February 2009 over charges of "facilitating" the Mumbai terror attack and they had been in jail since then.
India had earlier taken strong exception to grant of bail to Lakhvi last year, days after the December 16 terrorist attack on the Army Public School in Peshawar city of Pakistan.
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The Islamabad High Court on December 29 last year suspended the detention order but the order was restored later.
Lakhvi is accused of masterminding the Mumbai terror attack in November 2008 in which 166 people, many of them foreigners, were killed and hundreds others wounded.
Meanwhile, the US said it was monitoring the developments closely. Jen Psaki, State Department spokesperson, said in Washington on Friday that the US hoped Pakistan would keep its commitment to bring the perpetrators of the Mumbai terrorist attack to justice.
However, she declined to speculate on the outcome of the ongoing case.
"The government of Pakistan has pledged its cooperation in bringing the perpetrators - financiers, and sponsors - of the Mumbai terrorist attack to justice and we urge Pakistan to follow through on that commitment," said Psaki.