Defence Minister Antoni Macierewicz said previous inquiries that blamed human error and bad weather were riddled with "mistakes".
He said the crash near Smolensk might have been caused by an explosion.
Polish officials earlier accused Russia of withholding key evidence, something denied by Moscow.
Announcing the new investigation, Mr Macierewicz suggested that the presidential plane had "disintegrated" between 15 and 18 metres (49-59ft) before crashing in western Russia on 10 April 2010.
"There is no doubt that these circumstances are not only a sufficient reason, but one that makes it compulsory to re-examine this tragedy," the minister said.
He questioned the results of previous Polish and Russian investigations.
Among those who died were top state officials, many of whom belonged to the now governing Law and Justice party led by Jaroslaw Kaczynski - the late president's identical twin brother.
The party has never accepted the previous inquiries that concluded the Smolensk crash was an accident.
Commenting on Poland's move, Russian foreign ministry spokeswoman Maria Zakharova said she hoped "this is not linked to politics".
"This hope is a faint one, but it still exists," she added.
Relations between Poland and Russia have been strained over the continuing conflict in Ukraine's south-east and the annexation of the country's southern Crimea peninsula by Moscow in 2014.
Correction 25 February 2016: This report has been amended to clarify the findings of the different investigations into the crash.
Poland has launched a new investigation into the 2010 plane crash in Russia, in which President Lech Kaczynski and 95 other people were killed.