Dozens of non-governmental organisations (NGOs) in Russia have been required to suspend operations after missing a deadline to register.
President Putin said "foreign puppet masters" controlled some NGOs
Human Rights Watch is one of the bodies that have failed to clear the red tape in time - but it vowed to keep working.
Moscow says the new law, allowing monitoring of foreign and domestic NGOs, will stop foreign governments using them for political purposes.
Critics say the law is designed to silence independent thought in Russia.
There are estimated to be between 200 and 500 NGOs operating in Russia.
Registration officials said 80 had registered under the new law by Wednesday's deadline and 72 other applications were still being examined.
The other groups will have to suspend their activities but can continue to employ and pay staff.
Russian officials say they do not intend to close down a large number of NGOs because they have not registered, as had been feared when the law was passed in April.
NGOs can still apply to register.
Organisations that are affected by the new law include adoption agencies, social welfare groups and human rights organisations.
One of the best-known groups, Human Rights Watch (HRW), says it made repeated efforts to register, but that officials constantly changed the list of documents they require.
It said it would continue operating, despite the order to suspend activities.
"It's not clear how we're going to work, but we will work," said Alison Gill, director of HRW's Moscow office.
The head of the new registration service said many organisations had submitted applications riddled with errors.
Sergei Movchan, director of the Federal Registration Service, said on Monday that some NGOs "want to build up an image as victims of repression in Russia".
He said the purpose of the registration law was less sinister: "We look at the aims and purposes announced by the organisation and what funds are being spent on them and whether these funds are being spent on these aims and purposes. This is all."
The BBC's Russian affairs analyst, Steven Eke, says the controls and monitoring imposed on Russian NGOs are much harsher than those on foreign agencies.
Many have reported coming under increasing pressure from the police, security services and apparently co-ordinated campaigns of physical harassment, our correspondent says.