"He also expressed strong support for the crown prince's ongoing efforts to initiate the national dialogue and said that both the opposition and the government must compromise to forge a just future for all Bahrainis," a White House statement said.
"To create the conditions for a successful dialogue, the president emphasized the importance of following through on the government's commitment to ensuring that those responsible for human rights abuses will be held accountable."
Obama's meeting with the crown prince came shortly after Iranian President Mahmoud Ahmadinejad said that Tehran had a plan for Bahrain and said the main problem was the presence there of the US Fifth Fleet.
Predominantly Shiite Iran, which has vocally supported most of the uprisings across the Arab world, harshly condemned the crackdown in Bahrain, which in turn accused Tehran of meddling and fanning confessional unrest.
Earlier the Bahraini crown prince, viewed by US officials as a key player in efforts to mitigate the political crisis, met US Secretary of State Hillary Clinton to discuss King Hamad's plan for a national dialogue.
"It is very significant to have these discussions, to hear directly from the crown prince (about) the plan that Bahrain is pursuing," Clinton told reporters.
"Bahrain is a partner and a very important one to the United States and we are supportive of their national dialogue and the kinds of important work that the crown prince has been doing in his nation, and we look forward to it continuing."
The crown prince said that it was a "great pleasure" to be in Washington during a "challenging time" for the kingdom.
"We are committed to reform in both political and economic spheres," he said.
Oil-rich Bahrain has long been a key US ally in the Gulf region, and hosts the headquarters of the US Fifth Fleet.
But a brutal crackdown by security forces against the Shiite protesters earlier this year put Washington in a tough spot.
The Obama administration also appeared surprised when a Gulf Cooperation Council force led by its ally Saudi Arabia and the United Arab Emirates entered Bahrain in March, after a month of anti-regime protests.
On June 1, Bahrain lifted the state of emergency it imposed in mid-March during the crackdown on pro-democracy Shiite-led street demonstrations, which erupted a month earlier.
But Bahrain's royal family, drawn from its Sunni minority, has not called for a withdrawal of the Arab troops from neighboring Gulf states who were brought in to help deal with the unrest.