Congolese soldiers and UN peacekeepers have been conducting joint operations in eastern Congo targeting fighters from the Democratic Forces for the Liberation of Rwanda (FDLR).
"The government should take urgent action to end these abuses," Woudenberg said.
"A military operation that targets the very people the government claims to be protecting can only lead to disaster."
A government spokseman rejected the charges as "ridiculous".
Lambert Mende, the information minister said: "We are going to put an end to all these [accusations]".
"This is nearly word for word the statement of the FDLR. We now have proof that HRW supports the FDLR.
"I think there will be consequences. But first the government will meet to decide what measures to take," he said.
The FDLR mostly retreated into the bush when the government, backed first by Rwanda's army and then by the UN, launched the offensive.
But tens of thousands of civilians have been displaced during the operations and the FDLR has retaken much of the ground they initially lost.
UN security council envoys flew to Goma in eastern Congo on Monday to aid a UN drive to help resolve years of conflict in the region and allow the 17,000-strong UN force there to leave.
"Security council members should tell President Joseph Kabila that UN peacekeepers cannot support military operations in which war crimes are being committed," Woudenberg said.