Trump also has a super PAC benefiting him, which has only $500,000 in the bank. Two remaining pro-Trump groups are yet to disclose their fundraising position, but will do so next month.
The Clinton campaign - with around 700 members of staff, compared to Trump's 70 - is planning to spend $117 million between now and Election Day on an onslaught of television advertising.
The New York Times described Trump's deficit as "the worst financial and organisational disadvantage of any major party nominee in recent history".
Presumptive nominee Mitt Romney also had a money deficit when he raced against Obama in 2012, however Romney's campaign raised millions more than Trump during the same period.
Trump appeared to dismiss any fundraising concerns on Tuesday morning, telling NBC's Today he is willing to "do what I did in the primaries".
"I spent $55 million of my own money to win the primaries. Fifty-five, that's a lot of money by even any standard," Trump said. "I may do that again in the general election."
The real estate mogul, who has loaned his campaign about $46 million since launching last year, added that he has "a lot of cash" but said that "it would be nice to have some help" from the party. "I'm having more difficulty with some people in the party than I have with the Democrats," he said.
Trump's senior adviser, Tana Goertz, said she was not concerned. "Guess what - Mr. Trump is a billionaire," she told CNN on Monday. "Money is not a problem."
His campaign spokesperson Hope Hicks also denied there were any money issues prior to the report being released: "There are no fundraising concerns whatsoever. The money is pouring in, and Mr. Trump has received tremendous support," the 27-year-old said via an email last week.
After Trump's campaign cash crisis was revealed, Twitter users were quick to mock the billionaire businessman, and it wasn't long before the hashtag #TrumpSoPoor began trending.
The financial report was filed just hours after Trump sacked his hard-charging campaign manager, Corey Lewandowski, amid concerns among allies and donors about his ability to run a competitive race. It's thought the dramatic shake-up is designed to calm panicked Republican leaders after a tumultuous period, marked by infighting and rumours.
"The campaign is grateful to Corey for his hard work and dedication and we wish him the best in the future," a statement read.
