Kuldip Nayar (long time advocate for the victims of the 1984 pogroms) reviews the Nanavati Commission report and finds that it does not go far enough:

I find that the Justice G.T. Nanavati Commission Report on the 1984 anti-Sikh riots is not a fair document. The judge traces events more or less accurately, yet he does not come to the obvious conclusion.He goes as far as to say: “The systematic manner” in which the Sikhs were killed indicated that “the attacks on them were organised”. But he holds back when, as a judge, he should have gone further to probe who organised these systematic attacks. [cite]

Nayar illustrates how Nanavati illuminates the role of powerful political actors in setting the 1984 Delhi pogroms into motion, but he does not inquire as to who these political actors were.

Nanavati says there is evidence to show that on October 31, 1984, the day Mrs Gandhi was killed, “either meetings were held or the persons who could organise attacks were contacted and were given instructions to kill Sikhs and loot their houses and shops.”  Nanavati also says that attacks were made “without much fear of the police, almost suggesting that they were assured that they would not be harmed while committing those acts and even thereafter.”

On that command, hundreds of people went to the streets of Delhi with weapons and inflammable material like kerosene oil, petrol and white powder. According to the Nanavati report, “the male members of Sikh community were taken out of their houses. They were beaten first and then burnt alive in a systematic manner. In some cases tyres were put around their necks and then they were set on fire by pouring kerosene oil or petrol over them.”

Jagdish Tytler, Sajjan Kumar and Dharam Dutt Shastri, named by Nanavati, could only be operators. At worst, they could have conveyed instructions. But who gave the instructions? Who were the ones who did it? Where did they gather to hatch the plan? Who were these shadowy figures, behind-the-scenes, confident that their instructions would be carried out? [cite]

By implication, this raises another important point. Why were people like Tytler and Kumar on the cabinet in the first place? What did Sonia Gandhi gain by having them there? They were hardly powerful political figures, nor were they doing important jobs. Two thoughts: (1) Maybe Sonia has a strong personal loyalty to these two, and sees them as having done no wrong (2) Perhaps they are owed something by actors more powerful and are being rewarded for holding secrets. I realize that option #2 sounds conspiratorial, but I want to point out the oddity in their presence. Why were these guys in cabinet at all? What does that mean in terms of the political logic of this government?

BTW, I disagree with one finding in the report. Coverage of the report makes it seem like Nanavati finds that the whole thing was organized just after Indira was shot. I find that highly implausible. The Indian bureaucracy moves very slowly. To get this many people, this many resources, and this much information together is something that cannot happen in just a few hours. It is far more likely that this plan was in place long before, and was just waiting to be executed.