Clarence House said the move would “only inhibit” the prince’s ability to express concerns.
In one letter to the prime minister, the prince said the armed forces were being asked to do a challenging job “without the necessary resources”.
Release of the letters follows a decade-long campaign by the Guardian.
The 27 letters to seven government departments on wide-ranging subjects, including the dominance of supermarkets, badger culling and the herbal medicine sector, were written between September 2004 and April 2005.
A government veto on publication was declared unlawful by the Court of Appeal last year – a decision which was upheld by the Supreme Court in March.
In one letter to the prime minister from September 2004, the prince expressed concern that the Army Air Corp’s ability to deploy equipment was being “frustrated by the poor performance of the existing Lynx aircraft in high temperatures”.
He added: “Despite this, the procurement of a new aircraft to replace the Lynx is subject to further delays and uncertainty due to the significant pressure on the Defence Budget.
“I fear that this is just one more example of where our Armed Forces are being asked to do an extremely challenging job (particularly in Iraq) without the necessary resources.”
The then Prime Minister Tony Blair replied a month later saying he found the prince’s letter “constructive and thought provoking” and that the limitations of the existing Lynx helicopters were recognised by the Ministry of Defence.
In February 2005, Prince Charles wrote a letter to Mr Blair in which he said the “dominant position” of retailers was the “single biggest issue affecting British farmers and the food chain”.