He, Prime Minister Donald Tusk and the president's twin brother, Jaroslaw, were among the dignitaries to receive Mr Kaczynski's coffin at a military airport in Warsaw after its repatriation from Smolensk.
The casket, draped in the red-and-white Polish flag, was carried across the tarmac by soldiers and placed before Catholic clerics who led a short prayer service before mourners took turns to kneel before the coffin and pay their respects.
Crowds of Poles lined the streets of the city, standing silently as the president's body was driven under military escort to the presidential palace, where it will be available for public viewing.
Thousands had gathered in front of the building, carrying flowers, candles, Polish flags and portraits of the deceased.
Some wept, others stood in silent reflection. As the president's body arrived, they softly began to sing the Polish national anthem.
Church services to honour their memory were earlier held across the country, as was a two-minute tribute, with church bells and police sirens.
'A great patriot'
Jaroslaw Kaczynski, Poland's former prime minister, had earlier travelled to Russia to help identify his twin's body.
Lech Kaczynski's brother, Jaroslaw, was among the mourners at the airport
The brothers' strong nationalist, conservative agenda divided opinion in Poland, but the BBC's Adam Easton in Warsaw says the president's supporters and opponents have joined together in paying tribute to him.
Boguslaw Staron, a 70-year-old from Warsaw, described Mr Kaczynski as "a great patriot".
"He taught Poles how to respect our traditions, how to fight for our dignity, and he made his sacrifice there at that tragic place," he said.
Poles gathered in town squares and in the streets at midday (1000 GMT) and stood silently to mark the tragedy, as church bells rang and emergency sirens wailed around them.
The president had been flying to Russia along with his wife, the heads of the army and navy, MPs and senior historians to mark 70 years since Soviet forces massacred more than 20,000 Poles near Katyn.
Russia has declared Monday a day of mourning and Russian Prime Minister Vladimir Putin, who visited the crash site with Polish counterpart Donald Tusk, said he would oversee the inquiry.
Russian and Polish investigators have recovered the flight-data recorders and are carrying out a joint inquiry.
Soviet secret police shoot dead more than 20,000 Polish prisoners-of-war, drawn mainly from the political, military and cultural elite
For 50 years, Soviet authorities blame Nazis for slaughter
In 1990, Soviet leader Mikhail Gorbachev admits Soviet responsibility
Vladimir Putin's invitation to memorial seen as attempt to resolve issue, which has continued to blight Polish-Russian relations
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