Questioning by German prosecutor Detlev Mehlis "is continuing. It should finish today (Thursday), and we do not know when (he) will return", the official said on Thursday.
Few details on the mission have been released by either the United Nations or the Syrians although it is expected that Mehlis will return to neighbouring Lebanon, where his commission of inquiry is based.
Syria is satisfied with UN investigators' handling of meetings with Syrian officials to hear testimony on al-Hariri's assassination, a Syrian source said on Wednesday.
"We are comfortable with the manner in which the meetings are being conducted," the official said on the second day of interviews at a hotel near the Syrian-Lebanese border.
The official declined to specify what questions were raised during the investigation, which Syrian media have said they fear might be politicised.
Another source said legal experts had been attending the meetings, whose records are being minuted in Arabic and signed by members of the UN team and the witnesses. He said the unidentified officials were testifying "in their personal capacities and not as officials".
Some Lebanese have blamed Syria, the dominant power in the country for nearly three decades, for the 14 February attack that killed al-Hariri and 20 others. Damascus has denied any role.
Deputy Prime Minister Abdullah al-Dardari said on Tuesday that Damascus had "nothing to worry about" and reiterated that it would offer the team, headed by German Prosecutor Detlev Mehlis, unfettered cooperation.
A car bomb killed Rafiq al-Hariri
on 14 February this year
Syria, which denied any role in the murder of al-Hariri, agreed last week to allow Mehlis' visit after being accused of not cooperating with the investigation, which began in June.
The investigating team arrived in Syria on Tuesday to hear testimony from Syrian officials, who according to sources in Beirut, comprise mainly officers involved in Lebanon's security about the time of the killing of al-Hariri.
The officials include Rustom Ghazali, chief of intelligence in Lebanon, and senior aides Mohammad Khallouf and Jamae Jamae, the sources in Lebanon have said.
Al-Hariri's killing sparked mass anti-Syrian protests in Beirut that forced Damascus to bow to world pressure and end its military presence in Lebanon in April.
Meanwhile, police and soldiers cordoned off a plush commercial center near the Lebanese Foreign Ministry after officials reported a bomb threat.
Explosive experts and police dogs searched the Center Sofil in the Ashrafiya district, where a bomb exploded last Friday, killing one person and wounding 23 others.
Security officials did not immediately give the source of the threat, but the LBC television station reported that an employee in a bank in a different part of the city had received a call saying a bomb would explode at Center Sofil.