Rasmussen said Afghan leaders and international force commanders would meet Thursday to discuss planning the 2014 drawdown.
Afghan President Hamid Karzai has said he'd leave signing a status of forces agreement with NATO allies to whoever takes his place after an April election. Rasmussen said planning operations were delayed without the agreement.
U.S. President Barack Obama spoke by phone Tuesday with Karzai, saying it was "unlikely" both sides would sign a bilateral security agreement defining post-2014 military options.
Future military operations may involve training, advising and assisting Afghan forces as they work to take on more national security responsibilities.
Rasmussen said without a bilateral agreement between the United States and Afghanistan, there won't be a complementary agreement between NATO and Afghanistan. If that's the case, he said, there will be no NATO forces operating in Afghanistan after 2014.
"This is not our preferred option," he said.
There are 11 candidates competing to take the place of Karzai, who's ineligible to compete because of term limits.