"In all we have documented the deaths of 45,048 people," Observatory director Rami Abdel Rahman told AFP, adding that more than 1,000 people were killed in the past week alone.
The Observatory, which relies on a network of medics and activists on the ground, said the real number of those killed since an uprising against President Bashar al-Assad erupted in March 2011 could run as high as 100,000, with both sides concealing many of their casualties.
The Britain-based watchdog reported fierce army shelling of a farming area in a village in the northern province of Raqa on Wednesday.
"At least 20 people, among them eight children and three women, were killed in shelling by regime forces of farmlands in Kahtaniyeh village, west of the city of Raqa," it said.
Amateur video posted online by activists showed several bloodied bodies, including at least one of a child, laid out on blankets in a house.
State television blamed "terrorists" -- a reference to rebels battling the regime -- for the attack.
Raqa has seen an escalation of violence in recent months as rebels have launched an assault to seize several areas of the province, strategically located on the Turkish border.
The Observatory also reported new clashes in the Palestinian refugee camp of Yarmuk in southern Damascus, scene of fierce fighting last week, and near Wadi Deif base in the northern province of Idlib, where it said 20 rebels were killed.
The UN High Commissioner for Refugees "estimates that if fighting in Syria continues, the refugee figure could reach 1.1 million by June 2013," a report said, double the current number of those registered by the United Nations.
In the past 24 hours, more than 1,000 Syrians crossed into Turkey, a Turkish foreign ministry official said on Wednesday, three days after a deadly regime air strike on a bakery in the central Hama province.
Brahimi arrived in Syria on Sunday to push a new initiative aimed at ending the bloodshed and getting the regime and opposition to the negotiating table.
A UN Security Council diplomat, however, said the veteran Algerian diplomat had received no support from any of the warring parties.
"Assad appears to have stonewalled Brahimi again, the UN Security Council is not even close to showing the envoy the kind of support he needs and the rebels will not now compromise," the diplomat said on condition of anonymity.
Opposition activists also blasted Brahimi.
"Brahimi's arrival in Damascus to discuss a new political initiative to solve the crisis caused by the regime... has not put a stop... to massacres," said the Local Coordination Committees, a grassroots network of anti-regime activists.
Brahimi is to hold talks on Saturday with Damascus ally Moscow, Russia's Deputy Foreign Minister Mikhail Bogdanov told the ITAR-TASS news agency.
The Russian foreign ministry said Brahimi himself had requested the meeting.
Foreign Minister Sergei Lavrov said Moscow was pushing Brahimi to ensure that the warring sides commit to a June peace plan that calls for a transition of power without making an explicit demand on Assad to step down.
Syria's deputy foreign minister, Faisal Muqdad, was already in Moscow for talks on Wednesday.
ITAR-TASS separately reported, quoting a source, that a "Syrian government delegation" -- whose members it did not name -- will meet with Lavrov in Moscow on Thursday.
The French daily Le Figaro said a solution in the offing would involve Assad staying in power until 2014 while preventing him from further renewing his mandate.
In a new setback for Assad, Syria's military police commander General Abdel Aziz Jassem al-Shallal announced his defection in a video posted online Wednesday, saying the army had "deviated" from its mission of protecting Syria.