Russian combat aircraft have carried out a second day of airstrikes against Syrian rebel forces as Moscow admitted it had targeted groups other than Islamic State in coordination with the government in Damascus.

As Vladimir Putin travelled to Paris for talks with French president Francois Hollande, the Russian president seized on US and western disarray and insisted that Russia was targeting Isis.

But Moscow appeared to admit it was striking more widely as American-backed rebels reported that they had been hit.

The US accused Russia of launching “indiscriminate military operations against the Syrian opposition” and the White House spokesman Josh Earnest said the airstrikes had targeted areas where there were “few if any” Isis forces.

Pentagon officials urged the Russian military on Thursday to focus its airstrikes in Syria on Isis fighters rather than opponents of Syrian president Bashar Assad, US administration officials said.

“What is important is Russia has to not be engaged in any activities against anybody but [Isis],” secretary of state John Kerry said. “That’s clear. We have made that very clear.”

Meanwhile, Russian and US military commanders began “de-confliction” talks to try to ensure their air forces did not inadvertently clash while conducting overlapping air campaigns. But a videoconference between Pentagon officials and their Russian counterparts ended without clear decisions on avoiding potential clashes between pilots.

Iran said it backed the Russian intervention, while unconfirmed reports that Iranian forces were also being deployed in Syria heightened tensions and deepened confusion over the escalating crisis.

Speaking ahead of his talks with Putin, Hollande said airstrikes in Syria should target Isis exclusively.

He said it was essential to ensure that “the strikes, regardless of who is carrying them out, target Daesh and not other groups”, using the Arabic acronym for the Islamist group.

The developments appeared to support the widely held belief that Russia’s real purpose is to bolster the regime of Bashar al-Assad and stave off western demands that he step down to make way for a political solution to the bloody four-and-half-year-old conflict.

Russia’s move clearly risks counter-action by countries supporting the rebels. According to one independent analyst, that may have already begun, with the Qataris – acting with the agreement of Saudi Arabia – flying in planeloads of weapons to Turkish airbases. “I would expect a huge influx of weapons into the north to try to blunt any ground assault by the regime,” the analyst said. “The stakes are very high.”

The commander of the Liwa Suqour al-Jabal rebel group, which has received training from the CIA, said a camp in northern Idlib province was struck by about 20 missiles in two separate sorties. “Russia is challenging everyone and saying there is no alternative to Bashar,” said Hassan Haj Ali, a Syrian army captain who defected after the uprising began in 2011.

The Russian defence ministry said its planes hit 12 Isis targets, including a command centre and two arms depots, although the areas where it said the strikes took place are not held by Isis.

Syrian activists reported a number of airstrikes in the country’s north and centre, including in the province of Hama, which they said airstrikes hit locations controlled by another US-backed rebel group, Tajamu al-Izzah.

Al-Mayadeen, a pro-Assad Lebanese TV channel, reported that Russian aircraft launched 30 airstrikes against Jaysh al-Fateh, a powerful Islamist rebel coalition that includes Ahrar al-Sham and the al-Qaida-affiliated al-Nusra Front.

Significantly, Russia’s official line appeared to change on Thursday, with a spokesman for Putin saying Russia was going after other groups in addition to Isis. “These organisations are well known and the targets are chosen in coordination with the armed forces of Syria,” the spokesman said.

Russia, like Syria, says all opponents of Assad are terrorists. Sergei Lavrov, Russia’s foreign minister, earlier dismissed reports of targeting non-Isis positions, describing “the rumours” as unfounded. “Our targets are solely the positions of objects and equipment belonging to the armed terrorist group Isil,” Russia Today quoted Lavrov as saying.

Syrian civil defence volunteers put the total civilian death toll from Wednesday’s strikes on Homs and Hama at 40, including eight children. The volunteer group said thermobaric missiles had been used and claimed that they struck a public market, bread distribution point and administrative buildings in Homs, as well as civilian homes.

“We can’t believe an even more advanced military power has arrived in Syria to kill civilians,” said one civil defence volunteer in a statement issued by his organisation.

Syrian rebels launched attacks in northern Homs against Assad regime troops and pro-government civilian neighbourhoods using Grad rockets in what they said was retaliation for Russian airstrikes.

The US defence secretary, Ashton Carter, described Wednesday’s strikes as illogical and “doomed to fail”, telling reporters: “It does appear that they [the Russian airstrikes] were in areas where there were not Isil forces and this is precisely one of the problems with this approach.”

John Kerry, the US secretary of state, suggested he was prepared to welcome Russian military action in Syria only if it was directed against Isis. Appearing alongside Lavrov after their UN meeting, he said: “It is one thing obviously to be targeting Isil. We’re concerned, obviously, that is not what is happening.”

Iran officially threw its weight behind the Russian campaign on Thursday. A foreign ministry spokeswoman said Moscow had her country’s full support in the strikes against what she described as terrorist groups.

But there was no confirmation of a claim from Hezbollah sources in Lebanon that Iran – which plays a key role in Damascus but has been reluctant to commit it own combat forces – was sending hundreds of new fighters into Syria to bolster Assad. The Pentagon said it was looking into the reports.

Saudi Arabia, Iran’s regional rival, and Turkey, which is at odds with Tehran over Assad’s fate, are deeply unhappy about the Russian involvement. Iran has played an instrumental role in propping up Assad’s regime by supplying him with financial and military support.