The bill, that has already passed the first of three readings in the State Duma (lower house), would bar publication of graphic scenes of violence and restrict journalists' access to the scene of militant strikes.
The bill followed criticism of the media's actions during the Beslan hostage crisis in September, when more than 330 people died. Officials said journalists showed no restraint in publishing graphic pictures of dead and injured people.
Journalists in turn said official spokesmen at the scene lied about the number of hostages and the militants' demands, and were forced to seek information from unofficial sources - something the new law would make illegal.
Putin's intervention is likely to carry weight in the Duma where more than two-thirds of deputies come from the pro-Kremlin United Russia party.
It is also likely to fuel theories that his frequent vetoes or interventions against restrictive laws are a Kremlin ploy designed to improve his image. He has previously quashed laws restricting beer drinking, smoking, journalists' rights and demonstrations.
But Vedomosti reported that, though Putin's criticism might mean that the press part of the anti-terror draft would be withdrawn, other restrictive provisions would remain.
Under the law, security agencies could impose a 60-day security clampdown if they received information - even unconfirmed - that an attack was being planned.
The bill was one of many measures proposed to tighten Kremlin control after Beslan.