A New Zealander was on board the aid flotilla attacked by Israeli commandos in international waters.
Mr McCully said the New Zealand woman has not been harmed and is now in Israeli custody.
"We are pursuing all the usual lines of consular activity to make contact with her," Mr McCully said.
The attack by Israel on the aid flotilla in international waters has left at least 10 people dead and sparked international condemnation.
Israel's ambassador, Shemi Tzur, was summoned by Mr McCully to a meeting this morning.
Labour leader Phil Goff joined Mr McCully in condemning Israel's actions but stopped short of calling for Israel's ambassador to be expelled.
"Israel's Ambassador to New Zealand must be asked to account for the enforcement of the blockade into Gaza and the disproportionate use of force against those in the aid flotilla.
"A resolution to the conflict in the Middle East will not come about unless there is a readiness to compromise on Israel's part," Mr Goff said.
Mr McCully said the New Zealand Government condemns the violence and especially the loss of life in the attack.
"I am taking immediate steps to communicate the Government's concerns over this incident to the Government of Israel," Mr McCully said.
He said the New Zealand Government supports other countries in calling for a full investigation into the incident.
"Representatives from our Mission in New York are attending the emergency meeting of the United Nations Security Council and we will continue to follow their deliberations carefully," Mr McCully said.
"New Zealand calls for restraint from all parties in dealing with the aftermath of this incident. This violent event serves to underline the fact that the situation in Gaza is not sustainable.
"We urge an intensification of the efforts to find a solution to that, and the wider challenges in the region," he said.
The New Zealand Palestine Human Rights Campaign spokeswoman Janfrie Wakim said Mr McCully should expel the Israeli ambassador immediately.
She described the Israeli military's attack as "a disgraceful act of piracy and murder".
"We feel New Zealand should never have invited the embassy back here when it continually flaunts international law, the Geneva Convention and United Nations Resolutions - 70 of them," Ms Wakim said.
Asked if her group was aware of the identity of the New Zealander in Israeli custody, Ms Wakim said: "It came as a complete surprise to us but it is wonderful that a New Zealander is there."
The Israeli Embassy only reopened in Wellington in April, after an eight-year absence from New Zealand.
The embassy closed in 2002 for financial reasons, and the Canberra-based ambassador was accredited to New Zealand.
Relations between Israel and New Zealand chilled after two reported Mossad agents, Eli Cara, 50, and Uriel Kelman, 31, were caught and jailed for trying to illegally obtain New Zealand passports in 2004.
A third suspected Mossad agent was a former Israeli diplomat based in Europe, Zev William Barkan, 37, who stole the identity of a tetraplegic Aucklander to fraudulently obtain his passport.
*It was originally reported that activist Caoimhe Butterly was on board one of the boats in the flotilla. nzherald.co.nz has since learnt that the information was incorrect and Ms Butterly is onboard a second flotilla due to land at Gaza within the next few days.
NZ woman on board aid flotilla
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