The situation has arisen days after Washington found itself having to change course and promise a visa to Indian Prime Minister-Elect Narendra Modi after his landslide election win. Modi was barred from the United States in 2005.
The possibility of another Washington U-turn became apparent after Indonesia's second-largest party on Monday suddenly switched its support to Prabowo from frontrunner Joko "Jokowi" Widodo ahead of July 9 presidential polls.
Prabowo was once one of Indonesia's most reviled men, accused of kidnapping, human rights abuses and a coup attempt after the 1998 overthrow of his former father-in-law, the late President Suharto.
A New York Times report in March said that in 2000 the U.S. State Department denied the former general a visa to attend his son's university graduation in Boston, but has never said why.
Prabowo told Reuters in 2012 he was still refused a U.S. visa due to allegations that he instigated riots that killed hundreds just before Suharto's downfall. He has denied wrongdoing.
According to Amnesty International, Prabowo was dismissed from the Indonesian military in 1998 for his role, while commander of Special Forces Command (Kopassus), in the disappearance of political activists.
India's Modi was denied a U.S. visa in 2005 under the terms of a 1998 U.S. law which bars entry to foreigners who have committed "particularly severe violations of religious freedom."
He has been accused of links to religious riots in his home state of Gujarat in 2002 in which more than 1,000 people, mostly Muslims, died.
However, after Modi's party swept to victory in elections last week, U.S. President Barack Obama was quick to telephone his congratulations and invite the new leader of a country he has declared a vital strategic partner to the White House.
The State Department said Modi would be granted an A-1 visa accorded to heads of state. Modi has also has denied any wrongdoing and has never been prosecuted in India.
An A-1 visa carries with it diplomatic immunity and is issued automatically - unless opposed by Obama, who has the authority to deny entry to anyone who has committed "crimes against humanity or other serious violations of human rights, or who attempted or conspired to do so."
Asked if Prabowo would be treated the same as Modi if he won Indonesia's election, a State Department official responded with statements similar to those before India's poll result - saying the department did not discuss individual visa cases.
"Applicants traveling on official business on behalf of their government are subject to limited grounds of ineligibility under U.S. immigration law. However, we cannot speculate on the outcome of any visa application," he said.
The official added that the United States remained "committed to close relations with Indonesia and expect that relationship to continue."
Analysts believe that Prabowo, like Modi, would be granted a visa if he wins the election.
Ernie Bower, a Southeast Asia expert at the Center for Strategic and International Studies think tank, said that like this week's martial law declaration in Thailand, the Prabowo case is an unwanted headache while Washington is trying to forge stronger ties in Southeast Asia in the face of an increasingly assertive China.
"For the United States, it is most important to focus on the mandate of the Indonesian people. Washington must embrace and work with whichever candidate is elected."