Interesting. Does the Indian government have a legitimate complaint? There is a very wide spectrum of possibilities here. They range from the Indian government being horrible, through localised corruption, through the government having very legitimate concerns about foreign interference, through to AI India being corrupt and/or in league with western intelligence agencies.
It's not a question of legitimate complaint. They didn't complain, they froze assets and halted the organisation's activity. The question is whether or not the Indian government's actions are legitimate, and whether or not their stated reasons are true. On the later, it seems to be a clear no.
Many NGOs were NOT filing annual reports that they were supposed to be filing, and their compliance(even pre-2014 norms) were not ensured by the govt.
UPA have used these NGOs to instigate protests in various state governments as Congress lacked strong real regional political activities and lack grass-root touch with people.
It was visible with the strong presence of NGO activists in the unconstitutional body of National Advisory Council.
Even after modification of norms, these NGOs were given sufficient notice and warning to file their reports.
On failure to which govt took drastic measure.