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International Atomic Energy Agency Director Mohamed ElBaradei said the death of the IAEA's "main interlocutor" had made the inquiry more difficult.
Diplomats say the IAEA was dealing with Brig Gen Mohamed Suleiman before he was shot at a beach last month.
Opposition media in Syria described him as a top presidential security adviser.
Suleiman was reportedly shot dead by a sniper near the port city of Tartus.
Suleiman had responsibility for sensitive security issues, pan-Arab newspapers al-Hayat and Al-Sharq al-Awsat say.
The UN says samples taken from a desert site in Syria - which was bombed by Israeli warplanes a year ago - have so far shown no indication of nuclear material.
Tests inconclusive
Mr ElBaradei did not identify the murdered official during a closed-door meeting about the investigation into Syria's alleged nuclear activity.
However, a senior diplomat said Suleiman had escorted UN inspectors on their only investigative visit to the al-Kibar site in northern Syria in June.
"His murder made the IAEA's job that much harder," the diplomat told Reuters news agency.
"Suleiman knew what was what and had the ability to deliver things."
Earlier, Mr el-Baradei said the investigation into claims about Syria's alleged nuclear programme had so far proved inconclusive.
The al-Kibar installation was bombed by Israeli jets in September 2007. Israel and the US say the site was a nuclear plant in the making.
Damascus denies the claims but the ruins were bulldozed after the attack.
On Thursday, Washington queried what Syria had to hide with that action, and asked the IAEA for a fuller report of its investigation.
Damascus, for its part, accused the US of using "twisted logic" in pressuring his country, rather than condemning the Israeli attack.
Full results from environmental swipe samples taken in June from the bombed site are due to be released within 3 weeks.
(BBC)
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