Clark has taken to social media to make clear she remains focussed on her campaign, and the poll was the first of many.
One supporter commented on Clark's Facebook page that the straw poll "had me shaking my head - the top two were men. So frustrating!".
In response, Clark wrote, "the first of many polls...".
A majority of UN member states want the next secretary-general to be a woman.
The 15 council members decided not to reveal the results of their voting to "encourage", "discourage", or express "no opinion" about the 12 candidates.
Labour's foreign affairs spokesman David Shearer said Clark would have hoped for a better result, but still had a shot.
"Everybody was talking about a woman and an Eastern European, in fact, that hasn't panned out in terms of the first straw vote goes," said Shearer, who spent 20 years working at the UN.
"Who knows what will happen with the next one. I think everyone will sort of swallow hard and soldier on, and that's what they should do."
Despite the council's efforts at secrecy, the results quickly leaked out.
Clark reportedly received eight "encourage" votes but five "discourage" votes and two "no opinion".
The Security Council's five permanent members - the US, Russia, China, Britain and France - effectively have veto power over the candidates.
The third-placed Bokova had a number of discourage votes, Shearer noted.
"If she had those from the permanent five and Helen didn't, that is a very big distinction. And we don't know that. There are a lot of unknowns and a lot of vagaries out there. I think we've just got to accept that is how it will be until that final vote."
More candidates could enter the race as there is no deadline for nominations - former Australian Prime Minister Kevin Rudd has made a late bid and has requested that the Australian government formally nominate him.
Another informal poll is expected to take place next week followed by several more in August, and possibly September.
US Vice President Joe Biden, speaking during a visit to Auckland yesterday, said the United States was considering supporting Clark.
After bilateral talks with Prime Minister John Key, Biden said he had been amazed by the "non-partisan zeal" with which she was being promoted by Key.
"I was impressed. I thought she was his sister.
"But all kidding aside, we have a very high regard for your nominee and she is one who is being closely considered."