Afghan officials have said up to 70 people were killed in the strike.
Nato officials have confirmed civilians were injured but have not said whether any died.
"If civilians were killed, then I would naturally deeply regret that," Merkel said.
|Brown and Merkel called for a UN-sponsored conference on Afghanistan [Reuters]
Merkel and Brown also added their support to French calls for a UN-led conference on the future of Afghanistan which they said must be held as soon as possible.
"The high-level conference that we propose on Afghanistan is one that should meet before the end of the year, it should deal with the issues of security, governance and development," Brown said.
"It should follow the work that is ongoing in all our countries to look at what is the best pathway forward for Afghanistan."
Merkel said the plan called for the Afghan government to take on "an increasing number of responsibilities itself", adding that she had already consulted with Washington and Nato.
"We will help with training and civilian reconstruction but the goal is not to lose sight of a sustainable security structure in Afghanistan," she said.
"We must move forward decisively on this and as the Afghans take on more responsibility for their security, then the international engagement can be reduced."
The UN peacekeeping department said on Friday that it was planning a summit in Kabul in the spring of 2010.