The suggestion of modifications worried conservationists, who felt that the MPA already made too many concessions.
It already allowed fishing in crucial spawning zones and only required tagging of 1 in 10 fish for research.
Mr McCully said the considerations were part of the ongoing diplomatic process to get the marine reserve approved.
"When I said early in the piece that people were underestimating the challenge of getting 25 countries, each with different interests, to agree on this issue, I think people thought I was probably doing a bit of political positioning.
"I actually meant it, and its proving as difficult as I expected to be."
Asked whether he was optimistic about getting the reserve approved at the Hobart meeting, he replied: "No I'm not."
There were already fishing restrictions in the Ross Sea, including a quota of 3800 tonnes a year, but the New Zealand-US proposal would have moved vessels away from some historical fishing grounds and spawning areas in an attempt to make the fishery more sustainable.