However, she said, it was important to remember progress had been made. She pointed to Bamiyan, where the involvement of New Zealand's Provincial Reconstruction Team had led to great improvements in health, education and infrastructure.
"We are committed to seeing this through because we cannot afford to see Afghanistan turn back into a haven for terrorism that threatens us all."
Clinton said New Zealand forces were "highly regarded" and had played a critical role.
"New Zealand's contributions are far beyond what one would normally expect of a country the size of New Zealand."
There has been scepticism about whether the Afghan security forces will be ready to take over when the International Security Allied Forces begin to withdraw next year, but Clinton said the progress they had made was "more a positive story than a negative story."
New Zealand's role in Afghanistan has contributed to the warming of the relationship between New Zealand and the United States over the past decade - it was the first thing Clinton listed when talking about areas of co-operation between the two countries.
Yesterday, Clinton said Key's leadership had "revitalised" the relationship between the two countries. The US felt "a special kinship, a closeness to New Zealand and the people and we continue to look for our relationship to go from strength to strength".
Key said he had promised New Zealand would stick to its commitment to ISAF - but the April withdrawal, at least a year earlier than Australia and the US, had not disappointed her. "We are on the homeward leg now."