He criticised UK Governments for making "arbitary and unexpected" tax changes over the years, which have made the oil and gas giant less willing to invest in some areas of the United Kingdom Continental Shelf than others.
Asked if a vote for independence for Scotland next year could affect Shell's interest in the North Sea, Mr Henry stressed the company wanted stability in the tax regime above all.
Talking to journalists after Shell announced a 32% fall in third quarter profits, Mr Henry made it clear the North Sea faces stiff competition from other areas with the company set to make tough choices about where to invest.
As number two to the outgoing chief executive Peter Voser, Mr Henry will play a key part in this process.
Asked how the North Sea would fit in the company's plans he indicated Shell's views differed depending on which area of it is under discussion.
West of Shetland, where Shell is investing in the multi-billion pound Clair and Schiehallion projects with BP and other majors, is a favoured area.
"We have two great growth projects in Clair and Schiehallion, which are both significant investment activities at the moment," said Mr Henry. "Those assets will be quite important parts of our portfolio for a very long time to come I would expect."
Mr Henry said Shell has good gas assets in the southern North Sea, off eastern England, operated out of the Netherlands.
Noting Shell expects to increase the pace of disposals, Mr Henry appeared to indicate assets in the Central North Sea, off eastern Scotland, may be sale candidates.
He said: "We have central North Sea assets which are part of some of the operational challenges that we have. These are mature assets and we need to be thinking about future decommissioning."
Mr Henry added: "Mature assets are always part of a discussion about how long do we keep these but it's just part of a normal tail-end asset review."
Independents including Enquest have shown their appetite for North Sea acquisitions.
Shell has interests in more than 50 UK North Sea fields.
Asked about Scotland possibly voting for independence in the referendum next September, Mr Henry said: "We try to stay out of such geopolitics in general and reiterate that our wish and our need for investment is a long-term stable energy policy and fiscal framework. What we don't need is arbitrary and unexpected changes in fiscal regimes. I can't speak for Scotland, but the UK has a track record of exactly this, which has affected our own willingness to invest in the UK in the past."
Mr Henry indicated recent concessions by the UK Government have not affected the company's view.
Noting Clair and Schiehallion account for the bulk of Shell's current investment in Europe, he said directors believe European energy policy and potentially fiscal frameworks don't provide the stability needed.
"Almost all of our investment is going into a combination of North America and emerging markets," he noted.
Shell posted underlying profits of $4.5bn (£2.8bn) for the quarter to September, compared with $6.6bn in the same period last year.
Mr Voser, who is leaving Shell at the end of this year, said: "We are facing headwinds from weak industry refining margins, and the security situation in Nigeria."
But he said the company's flow of projects for 2014 and beyond was strong.
The company announced a third quarter dividend of $0.45 per ordinary share, up 5%, from 43 cents in the third quarter 2012.
Royal Dutch Shell A shares closed down 5%, 107.5p, at £20.765.
BP highlighted pressure on refining margins when it announced better than expected third quarter results on Tuesday.