The verdict by a court in Delhi comes after more than 20 judges heard the case and 160 prosecution witnesses and 40 defence witnesses presented their testimony.
Mr Mishra died in January 1975 in a bomb blast at Bihar's Samastipur railway station, where he had gone to attend a function. Four of the initial five accused belonged to Ananda Marg, a Hindu group.
The men accused include an advocate, Ranjan Dwivedi, who was 24 years old at the time of the murder, Santoshananda Avadhuta, Sudevananda Avadhuta and Gopalji.
A fifth accused in the case has died.
Except Gopalji, the others were also named as accused in the murder attempt on then Chief Justice of India AN Ray in Delhi in March 1975. While Santoshananda and Sudevananda were awarded 10 years rigorous imprisonment each, Dwivedi was sentenced to a four-year jail term in the case.
The case was transferred to Delhi on a Supreme Court order in 1979, following an application by then attorney general, and charges were framed against the men in 1981.
Last month, when the verdict was deferred, Mr Mishra's family said the wait did not matter to them since they believed the investigations were botched up in the first place.
"I was in Patna on the day of the incident. When my father was brought to hospital, I spoke to him briefly. He told me, 'Don't worry, I am fine. Nothing will happen to me'," said Mr Mishra's son Vijay Kumar Mishra.
"The investigations were faulty. I don't think the Anand Marg was involved at all," he had added.