Officers fired tear gas shells to disperse supporters of Mr Khan, who threw stones and bricks.
In a video address, the politician, 70, offered to sign a guarantee that he will appear in an Islamabad court on Saturday.
He added that there were security concerns as two militant attacks had previously taken place at the court.
Mr Khan claimed there was "no reason" for police to arrest him on Tuesday as he had taken protective bail until Saturday. He also said the government was determined to put him behind bars after previous failed attempts.