Brammertz said that his office was "unable to present all evidence to the court because some witnesses failed to appear".
Brammertz also urged Serbia to do more to co-operate with the Hague tribunal, a key condition of further progress towards European Union membership.
He was speaking in Belgrade, during his first trip to Serbia since taking office in January.
"I particularly insisted on the arrest of the four remaining fugitives," he told reporters after meeting with Vladimir Vukcevic, Serbia's special war crimes prosecutor.
"It is crucial that they are brought to justice as soon as possible."
Brammertz also said that he had been briefed on Serbia's efforts to arrest the fugitives, who include the Bosnian Serb leaders Radovan Karadzic and Ratko Mladic.
However, he said "progress is still needed in all of these areas".
The European Union hopes Brammertz will give a positive report on Serbia, which would allow it to offer the country a pre-accession pact and boost pro-EU parties in a parliamentary election on May 11.
The Netherlands, however, has indicated it will block any signing unless there are signs that Serbia is trying harder, particularly in the case of Mladic.
Rasim Ljajic, the minister of labour, employment and social affairs, and Serbia's key point of contact with the International Criminal Tribunal (ICT) in the Hague, said there was no indication that Brammertz was softer than Carla del Ponte, the former UN war crimes prosecutor.
Del Ponte had an eight-year tenure at the ICT and was known for her ruthless pursuit of fugitives.
Rasim Ljajic said he expected Brammertz, who is Belgian, to have a different style.
"The difference in the approach to the problem is evident," he told a Vecernje Novosti, a Belgrade newspaper.
"Brammertz himself said he would avoid politics and deal more with legal issues. My impression is he doesn't seek publicity for himself, which was not the case for del Ponte," he said.
The visit comes at a time when the popularity of both the EU and the Hague tribunal are at a low point in Serbia. Brussels' support for the secession of Kosovo in February stoked nationalist sentiment.
The government coalition collapsed one month later over whether Serbia should pursue EU membership despite the bloc's support for Kosovo.