One of the Prince's employee spent two years at the Cabinet Office while another was seconded to a rural policy team at Defra, the environment and food ministry, for 14 months, The Sunday Times reported.
Several current and former ministers said they had not been informed of the placements and expressed surprise and irritation at not being told.
"There are questions that need to be answered about who agreed it. I think it's undemocratic," a minister was quoted as saying by the paper.
Ministers said they were planning to raise the issue within government.
Secondments between government departments, businesses and charities are common, but they are usually transparent. By contrast, both the government and the Prince's office were reluctant to disclose details, the report said.
While confirming that three of the Prince's employees had been sent to work in Whitehall, his office refused to provide their identities or say what tasks they had undertaken. It also declined to reveal who had authorised the placements.
"All three secondments were suggested on the basis of professional development and the paperwork was arranged by the relevant HR departments," he said.
Sources close to the Prince said his staff and the government were "in constant contact to keep him up to speed on issues and current affairs".
Foreign and Commonwealth Office staff and members of the military are often seconded to the palaces to advise the royal family on overseas visits and ceremonial matters, but there is not known to be a precedent for secondments from the royal household to the government.
While Charles has previously been accused of using his position as the heir to the throne to lobby government, this is the first evidence of his potential influence within it in areas where policy is being decided.
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