The Yedioth Ahronoth newspaper quoted a ministry official as saying Motti Zaken, an adviser on Arab affairs at the internal security ministry, had met some of 2,200 prisoners held at two jails, among them Hamas legislators
Despite Israel's formal boycott of Hamas, the meeting was to "to assess their mood", the newspaper reported.
It was the first such reported contact between an Israeli official and Hamas, which now heads the Palestinian government since the January parliamentary elections.
Israel has jailed about a dozen Hamas members of parliament over alleged security offences.
Asked about the report, Yehuda Maman, the ministry spokesman, said Zaken had met "security prisoners" about two weeks ago "as part of his professional work". He declined to elaborate.
Israel, supported by the United States and the European Union, has blocked a flow of funds to the Hamas-led government since March in an attempt to force it to renounce the armed struggle, and to recognise Israel and past interim peace deals.
Hamas's charter calls for Israel's destruction, and the group says talks with the Israeli government will be a waste of time.
All but Russia have also refused any diplomatic contacts with Hamas officials, though Mahmoud al-Zahar, the Palestinian foreign minister from Hamas, said on Sunday he had met a European foreign minister during a recent tour of Arab countries.
European countries have also begun to challenge a US-backed freeze on funds to the Hamas government, which some fear has brought the Palestinian Authority close to collapse.