Justice A M Thipsay made the remark while hearing a bail application of Shamil, who was arrested in connection with an attempt on the life of a VHP member in 2012.
Shamil's father Saquib Nachan had been earlier arrested for his alleged role in the 2003 Mulund bomb blast case and alleged links with the banned SIMI.
After reading the witnesses' statements, which do not reveal Shamil's involvement, the judge said, "I find this very strange...The way FIR has been filed. Basically, you (police) have dragged him because of his father. All this attention is because of the father. All these sections under Maharashtra Control of Organised Crime Act and Unlawful Activities (Prevention) Act are attracted because of the father."
The High Court also criticised police for the manner in which witnesses' statements were recorded. "All the witnesses have gone on and on about things irrelevant to the case in hand. No statement is clear about the involvement of the accused. Such things throw doubt on the prosecution case," Justice Thipsay said.
The hearing would continue tomorrow.