However, the Vega had not disrupted the drilling process, Mr Seay said.
"We've had to keep an extra eye out for them which we'd rather not have to do and whenever you've got somebody in close proximity in a safety zone, the safety risks are heightened, so we've had to take extra precautions to mitigate that."
Anadarko had not asked government authorities for any assistance to remove the protest vessels, however they had informed them of their presence, he said.
"We've notified the authorities, we did that last week, of the fact that the Vega's been inside that safety zone, but we're not seeking any particular intervention as such, that's always a call for them to make and so far they've seen fit to not actually go out there."
After finishing drilling in the deep-water Taranaki basin, the Noble Bob Douglas would move down to the Canterbury basin, off the Otago coast to drill there early next year, Mr Seay said.
Prime Minister John Key told 3 News this morning that it was not up to the Government to disrupt the Oil Free Seas protest flotilla.
"It's the police actually and Maritime New Zealand that have responsibility for whatever actions they may or may not take.
"Our concerns are just simply that in this case, this company Anadarko can carry out the work that they've been legally granted authority to do so by the Government.
"At the end of the day, those protesters have a legal right to be there, providing they abide by the law.
"One of those vessels is not abiding by the law and that'll be a matter for the police to decide whether they take action."
Mr Key described last weekend's 'banners on the beach' protest against the exploratory drilling as "rent-a-crowd".
Piha hosted more than 1000 people last weekend to listen to speeches and watch a haka. Around 400 people joined the protest at Muriwai, 500 at Bethells Beach, and almost 750 at Raglan.
"There was a few hundred people wandering around," Mr Key said.
"It's just Greenpeace ringing up its members and getting them to come along, the Green Party had a few [people] there, fair enough, it's not tens and tens of thousands of people.
"Most New Zealanders were going about their business actually enjoying some of the things that the Government provides like roading and the likes."
The Green Party made up the protest numbers and "put the worst possible spin they can on everything", Mr Key said.