A militant group affiliated to Islamic State in Egypt, Sinai Province, said in a statement it had brought down the plane "in response to Russian airstrikes that killed hundreds of Muslims on Syrian land", but Russia's Transport Minister told Interfax news agency the claim "can't be considered accurate".
The Airbus A321, operated by Russian airline Kogalymavia under the brand name Metrojet, was flying from the Red Sea resort of Sharm el-Sheikh to St Petersburg in Russia when it went down in central Sinai soon after daybreak, the aviation ministry said.
"I now see a tragic scene," an Egyptian security officer at the site told Reuters by telephone. "A lot of dead on the ground and many who died whilst strapped to their seats.
"The plane split into two, a small part on the tail end that burned and a larger part that crashed into a rockface. We have extracted at least 100 bodies and the rest are still inside," the officer, who requested anonymity, said.
Both black boxes of the plane had been found, Mohamed Hossam Kemal, the civil aviation minister, told a news conference.
Kemal said communications between the plane and air traffic control before the crash had been normal and that nothing irregular had occurred before the accident.
"The plane did not request a change of route," he said.
Egyptian Prime Minister Sherif Ismail also told the news conference that there did not appear to be any unusual activity behind the crash but the facts would not be clear until further investigations had been carried out.
Ismail said 129 bodies had so far been removed and the chances of finding survivors were now near-impossible.
Bodies were being transported to various hospitals with 34 arriving in the Zeinhom morgue in Cairo early in the evening.
Islamic State, in a statement on Twitter, said it had brought down the aircraft.
Sinai is the scene of an insurgency by militants close to Islamic State, who have killed hundreds of Egyptian soldiers and police and have also attacked Western targets in recent months. Much of the Sinai is a restricted military zone.
Militants in the area are not believed to have missiles capable of hitting a plane at 30,000 feet. Islamic State websites have in the past claimed responsibility for actions that have not been conclusively attributed to them.
Russia, an ally of Syrian President Bashar al-Assad, launched air raids against opposition groups in Syria including Islamic State on Sept. 30.
Two of Europe's largest airlines, Lufthansa (LHAG.DE) and Air France-KLM (AIRF.PA), said they would avoid flying over the Sinai peninsula while awaiting an explanation on the cause of the crash.
Egyptian President Abdel Fattah al-Sisi promised Russia's President Vladimir Putin he would allow Russian experts to join the investigation.
The prime minister said a Russian team would arrive in Egypt later on Saturday night. The country is also preparing to receive the families of the victims.
Putin declared a day of national mourning for Sunday. The passengers included 214 Russians and three Ukrainians.
A middle-aged man in a gray overcoat, who gave his first name as Nayeel, wept as he spoke to reporters as he came out of a hotel near St Petersburg's Pulkovo airport, where a special reception center has been set up for families of the victims.
He said that his wife had been on the plane.
"At six am she sent me a text message saying: I’m boarding. God be with me.’ And that was it,” he said. The man said the rest of the family had already returned from a holiday in Egypt, but his wife had opted to stay on, which is why she was on the Saturday morning flight.
The A321 is a medium-haul jet in service since 1994, with over 1,100 in operation worldwide and a good safety record. It is a highly automated aircraft relying on computers to help pilots stay within safe flying limits.
Airbus said the A321 was built in 1997 and had been operated by Metrojet since 2012. It had flown 56,000 hours in nearly 21,000 flights and was powered by engines from International Aero Engines consortium, which includes United Technologies (UTX.N) unit Pratt & Whitney and Germany's MTU Aero Engines (MTXGn.DE).
Emergency services and aviation specialists searched the wreckage for any clues to the crash. Wreckage was scattered over a wide area.
"We are hearing a lot of telephones ringing, most likely belonging to the victims, and security forces are collecting them and putting them into a bag," the security officer at the scene said.
Russia's Investigative Committee said it was checking fuel samples from the aircraft's last refueling stop, in the southern Russian city of Samara, according to RIA news agency. Searches were being carried out at Moscow's Domodedovo airport where the airline that operated the plane is based.
Kogalymavia was founded in 1993, and was earlier called Kolavia. Its fleet consists of two A320s and seven A321s.
Russia and other former Soviet republics have relatively poor safety records, notably on domestic flights.
Some Russian air crashes have been blamed on the use of aging aircraft, but industry experts point to other problems, including poor crew training, crumbling airports, lax government controls and neglect of safety in the pursuit of profits.
The aircraft took off at 5:51 a.m. Cairo time (10:51 p.m. EDT) and disappeared from radar screens 23 minutes later, Egypt's Civil Aviation Ministry said in a statement. It was at an altitude of 31,000 feet (9,400 meters) when it vanished from radar screens.
Accidents at cruising altitude are one of the rarest categories of accidents but also among the most deadly, accounting for 13 percent of fatal incidents since 2005, according to Boeing.
Investigators would be looking into, among other things, the weather at the time, the pilots' experience, maintenance records, signs of a stall and any evidence of an explosion.
Experts consistently warn air accidents are usually caused by a cocktail of factors, both human and technical.
According to FlightRadar24, an authoritative Sweden-based flight tracking service, the aircraft was descending rapidly at about 6,000 feet (1,800 meters) per minute when the signal was lost to air traffic control.
France's civil aviation safety agency (BEA) said it would send a team to Egypt on Nov. 1 to join investigators from Germany and Russia. The United States Secretary of State John Kerry offered U.S. assistance, if needed, a spokesman said.