Justice J B Pardiwala ordered fresh trial while disposing of a plea by Amit's father, Bhikhabhai Jethwa.
The petition had alleged that 105 out of the total 195 witnesses had turned hostile, while five of them had complained of intimidation by Solanki.
The CBI itself had sub substantiated the slain activist's father allegation before the high court saying that it was true. The agency also said that of these 105, seven were eye-witnesses to the alleged murder.
"I am very sorry to say that the presiding officer (of the special CBI court) also failed in his solemn duty to reach the truth. The presiding officer also remained a mute spectator... And continued to witness the drama of mockery of justice," the judge said.
"Retrial shall commence at the earliest and shall proceed on day to day basis," Justice Pardiwala said adding that the CBI as well as Gujarat police must ensure full protection to all the witnesses.
The high court had stayed the trial in March after admitting Bhikhabhai's plea.
Dinu Bogha Solanki, former BJP MP from Junagadh, and his nephew Shiva Solanki are the main accused in the case. Both are out on bail.
Bhikhabhai had alleged that witnesses turned hostile because Dinu Solanki and Shiva Solanki threatened them.
The police and the CBI were not serious about ensuring protection of witnesses or probing their intimidation by the accused, the petition had alleged.
Jethwa had filed a public interest lawsuit against illegal mining in Gir forest, the last habitat of the Asiatic lions.
The HC had initially asked the CBI to re-investigate the killing after Bhikhabhai moved the court expressing dissatisfaction about the probe conducted by Gujarat police.
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