Emyr Roberts said Natural Resources Wales will be different from other bodies under the Welsh government.
He said it would be able both to regulate and offer independent advice.
It is being created through a merger of the Countryside Council, Environment Agency and Forestry Commission.
Dr Roberts, a former senior Welsh government official, takes up his new post on Thursday, as a Â£1bn gas-fired power station in Pembrokeshire faces an EU inquiry over part of its licensing.
Friends of the Earth Cymru has complained that the UK government has breached environmental regulations by allowing the site to discharge water in to the Cleddau estuary 8C warmer than the water is extracted.
Environmentalists say the case raises a question of what a licensing body that was answerable to Welsh ministers would do in a similar situation.
Dr Roberts said the case "underlines the need for one voice in this area".
"We will make sure there are systems in place to separate any advice from any other statutory obligations on us," he said.
He said: "Anything to do with the environment is very complicated, and the Welsh government is bringing forward legislation to try and simplify this over the next few years and I would be very keen for the new organisation to work with Welsh government on that.
"We need to collectively look at that - and not all of this is devolved either - which brings in a further complexity.
"The model that the Welsh government wants here is slightly different from other arms length organisations in that the expectation is that this body will work very closely with the Welsh government in developing policies, and their operational impact.
"So I think it will be a close relationship, but it will be an arms length relationship."
Dr Roberts, who is originally from Anglesey, joined the civil service in 1991 after previously working for the National Farmers' Unions.
Ministers say replacing the three organisations with a single body will save the taxpayer Â£158m over 10 years.
The chief executive of Wales' new environmental management body says it will work closely with ministers but will maintain its distance.