Trump is ahead with 743 delegates, according to Associated Press estimates. Cruz had 545 including the weekend's pickups, while Ohio Governor John Kasich lagged far behind at 143.
Colorado's 34 delegates are a small fraction of the 1237 needed to win the nomination but take on more significance than usual with a contested convention becoming more likely. The next Republican contest is in New York on April 20.
A new Fox News poll had Trump garnering 54 per cent support from likely voters in his home state.
Manafort, 67, who helped President Gerald Ford's delegate operation at the 1976 convention and managed Kansas Senator Bob Dole's 1996 presidential campaign, said Cruz was "not playing by the rules" and doesn't "care about the party".
"If they don't get what they want, they blow it up," said Manafort.
A Cruz spokeswoman said Trump's campaign was trying to distract from its lack of a ground game.
"It's no surprise that Trump's team will lash out with falsehoods to distract from their failure, as they have the entire time," said the spokeswoman, Catherine Frazier. "We have earned our success by working hard to build a superior organisation and are working within the process and rules that have been established - which has led now to four consecutive wins, 12 wins total."
Cruz's sweep in Colorado highlighted Trump's lack of a robust national organisation as a political novice.
Manafort said Trump's campaign wasn't "playing in Colorado" and had succeeded with efforts with Alabama, Michigan and Nevada. Trump is running his own campaign and "was doing very well on a model that made sense, but now, as the campaign has gotten to the end stages, a more traditional campaign has to take place," he said.