Initial reports from Egypt said the pilot of the Kogalymavia airline had asked to make an emergency landing.
But minister Hossam Kamal said there had been no sign of any problems on board the flight.
Lufthansa and Air France-KLM said they would avoid the route while the cause of the crash was investigated.
A claim by a group allied to the so-called Islamic State (IS) in Sinai that it brought down the plane has been dismissed by Russia and Egypt.
The flight came down early on Saturday, shortly after leaving Sharm el-Sheikh for the Russian city of St Petersburg.
Russian authorities say the plane was carrying 217 passengers, including 25 children. There were seven crew members on board.
Egyptian officials had said 214 of the passengers were Russian and three Ukrainian, but Russian officials said at least one of the victims was from Belarus.
On Saturday morning, Egyptian aviation official Ayman el-Mokadem, who the country's media say is heading an investigation into the crash, said flight KGL9268 had asked to land early because of a technical failure.
But Mr Kamal told a press conference this was not the case.
"Up until the crash happened, we were never informed of any faults in the plane, nor did we receive any SOS calls," he said.
All contact with air traffic control had been normal, and pre-flight checks showed no problems, he added.
Egypt's civilian aviation ministry said the plane had been at an altitude of 9,450m (31,000ft) when it disappeared.
Security experts say a plane flying at that altitude would be beyond the range of a shoulder-launched surface-to-air missile (Manpad), which Sinai militants are known to possess.
Wreckage was found in the Hasana area of Sinai and the plane's two black box recorders were removed, Mr Kamal said. One of the instruments logs cockpit recordings and the other registers flight data.
German carrier Lufthansa said it would avoid flying over the Sinai peninsula "as long as the cause for today's crash has not been clarified". On Saturday evening, Air France-KLM said it was following suit.
British Airways and easyJet said their routes were regularly reviewed, but that they had no plans to alter their routes to and from Sharm el-Sheikh.
Sinai has an active militant network, and on Saturday afternoon, jihadis allied to IS made a claim on social media that they brought down flight KGL9268.
Russian Transport Minister Maksim Sokolov told Interfax news agency that "such reports cannot be considered true". No evidence had been seen that indicated the Airbus A-321 plane was targeted, he said.
This hotel near St Petersburg airport has become a gathering point for relatives of those on flight 9268. There are medics here to help them, and we saw an Orthodox priest. Some have been giving DNA samples, to try to identify their loved ones.
In the lobby, men from the investigative committee are huddled over files and phones - beside cabinets full of souvenirs. For some reason, riot police are patrolling the corridors too.
Occasionally, someone emerges red-eyed from the room where officials are passing on what information and answers they can to relatives. But it's still impossible to say why this happened.
A spokeswoman for the airline says the pilot was experienced, the Airbus plane had been through all its safety checks. But there are a lot of people here with urgent questions about why their friends and relatives are not safely home tonight after a holiday in the Egyptian sun.
Russian President Vladimir Putin has declared Sunday a day of mourning.
He has ordered an official investigation into the crash, and a commission headed by Mr Sokolov left for Egypt on Saturday afternoon.
The office of Egypt's prime minister said 129 bodies had so far been recovered and were taken to Cairo.
One un-named official described a "tragic scene" with bodies of victims still strapped to seats.
The plane appeared to have split in two, he told Reuters, with one part burning up and the other crashing into a rock.
05:58 Egyptian time (03:58 GMT): flight leaves Sharm el-Sheikh, the Egyptian cabinet says in a statement
06:14 Egyptian time (04:14 GMT): plane fails to make scheduled contact with air traffic control based in Larnaca, Cyprus, according to Sergei Izdolsky, an official with Russia's air transport agency.
06:17 Egyptian time, approx (04:17 GMT): plane comes down over the Sinai peninsula, according to Airbus
11:12 Egyptian time (09:12 GMT): flight had been due to land in St Petersburg's Pulkovo airport
A criminal case had been opened against Kogalymavia for "violation of rules of flight and preparation for them", Russia's Ria news agency reported.
Oksana Golovin, a spokeswoman for the airline, said the company did not see any grounds to blame human error.
She told a press conference that the pilot had 12,000 hours of flying experience. Kogalymavia did not yet know what caused the crash, she said, but the plane was "fully, 100% airworthy".
Police have searched the company's offices.
Mikael Robertsson, from the live flight tracking service Flight Radar 24, told the BBC that the plane started to drop very quickly, losing 1,500 metres in one minute before coverage was lost.
Local weather observations near the rescue scene suggest relatively benign conditions.