But many say the prosecutor's office has done the best job in difficult circumstances.
The verdict in the case of Mathieu Ngudjolo Chui, a former leader of the Nationalist Integrationist Front (FNI) militia group in the eastern Democratic Republic of Congo (DRC), was the second for the world's only permanent war crimes tribunal and its first acquittal.
Handing down the verdict, Judge Bruno Cotte stressed that the acquittal did not mean the court felt no crimes were committed but rather that witness testimony had been "too contradictory and too hazy".
"I think this is a wake-up call that the practices of the office and perhaps the structure needs to be looked at again," said Eric Witte, a former advisor to the president of the ICC who now works with the Open Society Justice Initiative.
"This isn't the first indication that there are problems with the Office of the Prosecutor's investigations," Witte told AFP after Ngudjolo's acquittal on Tuesday.
He said that new chief prosecutor Fatou Bensouda, who took over from Luis Moreno-Ocampo in June, had a "fantastic opportunity to make any changes that are needed."
Now 42, Ngudjolo was accused of using child soldiers to fight for him, including to carry out the massacre of 200 people at Bogoro on February 24 2003.
"I think a better built case with better evidence could have resulted in another verdict," said Geraldine Mattioli-Zeltner, advocacy director of Human Rights Watch's International Justice Programme.
In the ICC's first verdict in March, the conviction of former Congolese militia leader Thomas Lubanga, judges slammed the office of the prosecutor for not having sufficiently "supervised" intermediaries charged with finding child soldiers.
There was a risk that the intermediaries had "persuaded, encouraged or assisted" witnesses to provide false testimony, judges said.
Already in October, the Washington College of Law, while recognising the court's successes, also noted problems and raised possible solutions.
The sharing of decision-making between different sections of the prosecutor's office was particularly criticised.
"The need for three leaders to reach consensus on all or almost all decisions is likely to result in inefficiencies in the conduct of the investigation," the report said.
The Office of the Prosecutor should also employ more investigators, the report said, for which the international community should make more funds available to the cash-strapped ICC.
The prosecutor's office must carry out more and more investigations of alleged war crimes and crimes against humanity at a time of economic crisis when donor nations are increasingly reluctant to stump up funds.
"There are perhaps some things to think about, but you can't blame it all on the prosecutor," said Montserrat Carboni, the International Federation for Human Rights' (FIDH) representative at the ICC.
The prosecutor has the difficult task of investigating crimes several years after they were committed and "they clearly need more means," said Carboni.
She noted that while judges were critical of the prosecutor's office during the Lubanga trial, this was not the case in the Ngudjolo case.
"An acquittal doesn't necessarily mean that the prosecutor has not done the work properly," said Sarah-Jane Koulen, an international criminal law expert at the Netherlands' Asser Institute.
"Perhaps it just shows that the judges are impartial and independent," she said.
"NGOs generally call for the head of those accused of war crimes at all costs and take offence when there's an acquittal," she said.
"But justice doesn't work like that." – Sapa-AFP