He was detained for four days in June and then deported after being accused of being a threat to the country's security.
Auckland student Mr Sooden, who made world headlines when he was held captive in Iraq in 2006, said he went to Israel with the aim of doing volunteer work for the International Solidarity Movement.
ISM describes itself as a Palestinian-led movement committed to non-violent resistance to Israeli occupation of Palestinian land.
Mr Sooden holds both New Zealand and Canadian passports, but was travelling on his Canadian passport at the time.
In a recent letter, MFAT told Mr Sooden that it would not have expected to be notified of his detention as he did not enter Israel on a New Zealand passport.
Mr Sooden said the response raised "serious questions" for New Zealanders with dual citizenship who travelled on a passport of their other nationality. "I am a New Zealand citizen, and I would expect the New Zealand Government to act to protect its citizens overseas."
Mr Sooden said he was assaulted and injured, threatened, held in solitary confinement, and denied the right to legal counsel and consular representation before being deported on June 18 last year.
In November 2005, Mr Sooden, Briton Norman Kember, Canadian James Loney and American Tom Fox, who were all working with Christian Peacemaker Teams in Iraq, were kidnapped by a group calling itself the Swords of Righteousness Brigade.
Mr Sooden, Mr Kember and Mr Loney were released after 118 days, but Mr Fox was shot dead while in captivity.
