In a letter to PINS chief executive Sir Michael Pitt, Nick Boles said he wanted to "restate very clearly the government's view of green belt policy and local plan examinations".
The letter follows the examination of Reigate & Banstead Borough Council's core strategy by inspector Martin Pike, whose report, published in January, found the plan sound subject to a series of modifications.
One of these was that the authority should "recognise that some loss of green belt to housing development will be necessary, in certain sustainable locations, to meet as far as is practicable the needs of the borough".
The plan proposes building at least 6,900 new homes up to 2027, with up to 1,400 homes on two green belt urban extensions.
The Tory-controlled council is due to consider adopting the draft plan at a meeting on 10 April.
However, Kathy O'Leary, the council's deputy chief executive, said the authority is now "considering the implications" of Boles' letter for the core strategy and "seeking advice" on the council's position.
Boles wrote that he was "disturbed" by the inspector's language, "which invited misinterpretation of government policy and misunderstanding about the local authority's role in drawing up policies in the draft plan".
He went on to say: "The (National Planning Policy) Framework makes clear that a green belt boundary may be altered only in exceptional circumstances."
Boles said "it must always be transparently clear" in inspectors' reports that, if authorities review and adjust green belt boundaries, it was their choice to do so.
The secretary of state would consider intervening in local plans, he added, if they are adopted where an inspector has recommended a green belt review not supported by the local authority.
Boles asked Pitt to circulate copies of his letter to all inspectors and "ensure they understand the need to choose their words carefully and reflect government policy very clearly in all future reports".
Reigate's Conservative MP Crispin Blunt, who had lobbied hard against the green belt release, told Planning that the letter represented "a huge victory". He said: "This is utterly unequivocal. The minister has said that the green belt trumps housing numbers, which is a sea change."
Blunt said he expected the authority's Tory councillors to "defend the green belt", rejecting the current strategy at the council meeting.
Catriona Riddell, the Planning Officers Society's strategic planning convener, said if the council follows this path and is backed by the secretary of state, it would have "huge implications", potentially opening the floodgates for other green belt authorities to adopt a similar stance.
Though she said in practice the letter was simply the government "distancing themselves from the decision about the need to release green belt", she said councils could conclude that it was saying green belt protection was more important than meeting housing need.
Ian Tant, a senior partner at consultancy Barton Willmore, said he was "concerned" by the letter's "political message" and said the inspector did not appear to have done anything wrong. He said: "There's a danger of the letter being taken by green belt authorities as an entitlement for them not to review their green belt boundaries."
A PINS spokesman said that "inspectors always take fully into account government guidance in respect of protecting green belt".