Many Gulf heads of state have said they will not attend this week's summit of US and Arab leaders at Camp David.
Their substitution with more junior leaders is seen by some analysts as a rebuff to President Obama's talks with Iran over its nuclear ambitions.
Saudi officials denied this, saying King Salman said he needed to stay home to oversee a ceasefire in Yemen.
The US said the king had spoken by phone to Mr Obama to voice "his regret at not being able to travel" to the US.
The talks in Camp David near Washington on Thursday are designed to reassure the Arab allies of US support on a number of issues including talks with Iran and instability in several Arab states.
They will now be largely attended by leaders at the ministerial level.
The official reason for the Saudi leader's absence is that the summit coincides with a humanitarian ceasefire in neighbouring Yemen, where a Saudi-led alliance is battling Shia Houthi rebels.
"I know there had been some speculation that this change in travel plans was an attempt to sent a message to the United States," White House spokesman Josh Earnest said.
"If so, that message was not received, because all the feedback that we've received from the Saudis has been positive."
The White House later said that President Obama had spoken by phone to King Salman on Monday and they had discussed preparations for the Camp David summit.
At Saudi Arabia's embassy in Washington, Saudi Foreign Minister Adel al-Jubeir told reporters the move was not related to any disagreement.
But diplomatic experts say it is a clear signal of Saudi displeasure with the US president and his negotiations with Iran over its nuclear programme.
"I don't think they have a deep respect, a deep trust for Obama and his promises. There is a fundamental difference between his vision of post-nuclear-deal Iran and their vision," Abdulkhaleq Abdullah, a professor of political science at Emirates University told the Associated Press news agency.
"They think Iran is a destabilising force and will remain so, probably even more, if the sanctions are lifted."
The BBC's security correspondent, Frank Gardner, said King Salman has never quite forgiven President Obama for cancelling the missile strikes on Syrian President Bashar al-Assad at the 11th hour in September of 2013, when King Salman was defence minister.
Separately, the tiny island kingdom of Bahrain, whose leadership has close ties to the Saudis, said that it would be sending its crown prince, Salman bin Hamad al-Khalifa, to the meeting.
A source familiar with the talks told the BBC that the Sultan of Oman and the President of the United Arab Emirates are both known to be very ill, and do not travel for non-medical purposes - and were not expected to attend.
The Kuwaiti emir, Sabah al-Ahmad al-Sabah, will attend the summit and has already arrived in the Washington area.
Qatar's emir, Sheikh Tamim bin Hamad al-Thani, is expected to attend as well.