"The administration is maintaining restrictions on specific activities and actors that contribute to human rights abuses or undermine Burma's democratic reform process," deputy national security adviser Ben Rhodes said, using Myanmar's former name.
Obama "is taking this step to advance our policy of promoting responsible economic engagement and encouraging reform that directly benefits the Burmese people," Rhodes said in a statement.
Obama in November suspended a ban on imports from Myanmar except gems. The sanctions formally lapsed last month after Mitch McConnell, the top Republican in the Senate, said it would be counterproductive to renew sanctions legislation.
Rhodes said that Obama "fully supported" the end of the broader ban.
But US lawmakers pressed to keep the decade-old ban on imports of gems, which often come from Kachin state and other conflict-torn areas.
Human rights advocates say that the lucrative trade has helped fuel the violence, with ethnic minorities seeing little of the profit from gems in their regions despite working under harsh conditions.
A US official said that despite changes in Myanmar, little was known about the gem trade but the military appeared to be in charge.
"There is virtually zero transparency on where that money is going," the official said on condition of anonymity.
Myanmar produces some 90 percent of the world's rubies and much of the trade is controlled by the military, which ruled the country from 1962 to 2011.
A US law passed in 2008, which cracked down on Myanmar-origin gems exported via third countries, estimated that $100 million in Myanmar's precious stones were coming into the United States annually at the time.
But the renewed US ban will not deprive Myanmar of other customers. The European Union in April ended all sanctions on Myanmar except weapons sales.
Neighbors China and Thailand have been major buyers of Myanmar's gems. A US official told Congress in 2011 that, despite Western bans, Myanmar was exporting more rubies and jade due to high demand in China.
Myanmar's President Thein Sein, a former general, has surprised even critics by embracing democratic reforms including allowing long-detained opposition leader Aung San Suu Kyi to enter parliament.
Myanmar has also eased restrictions on the media, freed political prisoners and reached out to ethnic rebels to end myriad conflicts.
But a key test will come in 2015 when Myanmar is scheduled to hold elections, meaning the military stands to lose real power for the first time.
Alarm has also grown overseas over violence against the Muslim minority, with at least 44 people killed in strife in March and thousands of people left homeless.
Representative Joe Crowley, a Democrat who spearheaded sanctions bills, said he supported the ban on gem imports.
He called for Myanmar to "release all remaining political prisoners, stop violence against minorities and undertake genuine constitutional reform."
"All the people of Burma deserve to carry out their lives in genuine freedom," Crowley said.
Obama paid a landmark visit to Myanmar in November, heralding what he sees as a signature international success story under his watch.