Datuk Seri Najib Tun Razak presented the share certificate to Lee, who arrived from London at 6.45am, at a breakfast at Seri Perdana, the Prime Minister''s official residence.
His wife, Datin Seri Rosmah Mansor, who is patron of the Badminton Association of Malaysia, gave Lee a watch as a personal present.
Lee beat his nemesis Lin Dan of China 21-17, 21-17 in 52 minutes in the singles final at the Birmingham Indoor Arena in England.
Najib, in his speech, said that he had been confident that Lee would beat Lin Dan because the Malaysian was more focused and sure of himself than he was in their Olympics final meeting.
Najib said that Lee had telephoned Rosmah, as had become his habit before a tournament, to get words of inspiration. She promised the shuttler a special prize if he won.
The Prime Minister hoped that the win would be the foundation for Malaysia to win the gold in the Olympic games to be held in London in 2012.
"This is my hope and the hope of 27 million Malaysians. This is our big ambition (in sports), our supreme dream that requires the effort of all to turn into reality," Najib said.
He also said that Malaysian players who had not been so successful at the All-England should not be too despondent.
Najib said that Koo Kien Keat and Tan Boon Heong should regard their defeat in the final to Danish pair Mathias Boe and Carsten Mogensen as a lesson to be used for future triumphs.
"The important thing is to strengthen ourselves. We must never be pessimist or negative, but always be positive," he said.
Najib had explained on his Twitter page why he was not declaring a public holiday after the All-England success.
He said that a public holiday would be very costly for the country.
"We have to work hard so that we can achieve more in future," Najib said.
Rosmah said that Lee''s win should inspire all Malaysian players, including the backup squad, to strive harder to improve their game.
The Prime Minister's wife said that Malaysia had to develop the secondliners to be world class players themselves to be victorious at the Olympics.
Also present were Youth and Sports Minister Datuk Seri Ahmad Shabery Cheek and BAM president Datuk Nadzmi Salleh.
Read more: PM presents PNB shares to Lee Chong Wei http://www.nst.com.my/nst/articles/PMpresentsPNBsharetoLeeChongWei/Article/#ixzz1GegwoOi3