An international outcry over the civilian death toll from the air war against pro-Iran rebels launched by a Saudi-led coalition in March last year prompted the White House to announce a review of US intelligence and logistics support earlier this month.
But Washington has trod a wary line, not wanting to strain already delicate relations with Riyadh, a key Middle East ally and partner in the US-led coalition battling the Islamic State group in Syria.
Votel told reporters travelling with him that he wanted to hear Saudi concerns.
"The first thing we are trying to do is listen to what they are telling us. It's important to maintain confidence in the relationship," he said.
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The official Saudi Press Agency reported that Prince Mohammed and Votel discussed defence cooperation and joint efforts in "combatting terrorism".
An October 8 air strike on a funeral ceremony in Yemen's rebel-held capital Sanaa which killed more than 140 people, most of them civilians, sparked a storm of criticism of both Saudi Arabia and its US ally.
In the summer, Washington cut the number of advisers deployed to a joint planning cell from 45 to five but the US Air Force stills provides air-to-air refuelling for Saudi bombers operating over Yemen.
The frictions over the air war in Yemen come with relations already strained.
Riyadh was angered by the US Congress's passage last month of a law allowing the families of 9/11 victims to sue the kingdom for alleged ties to the 2001 attacks that killed nearly 3,000 people. Saudi officials vehemently deny any involvement.