Peshawar High Court Chief Justice Dost Mohammad Khan questioned the legal grounds on which Baradar was released by Pakistani authorities.
He ordered authorities to inform the court about the laws under which Baradar was first arrested and then released by the government.
Even the President or the Prime Minister do not have the authority to free prisoners without due process, he observed.
Khan raised the issue while a two-judge bench was hearing a case related to "missing persons" or those detained without charge by security and intelligence agencies.
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Baradar was captured during a joint operation by Pakistani and American intelligence operatives in Karachi in 2010. He was the highest ranking of the 34 Afghan Taliban commanders freed by Pakistan to boost the stalled peace process in Afghanistan.
However, the provincial Chief Justice said Baradar should have been presented in court before his release.
Kabul believes Baradar is key to its efforts to kick-start the peace process as NATO combat troops prepare to pull out of Afghanistan by the end of 2014.