"The signed [agreement] can't be unsigned," Asfaw Dingamo, the Ethiopian minister for water resources, said, referring to the pact signed in May.
"But we hope to reach a consensus and I hope to do it very soon."
The five signatories have given the other Nile Basin countries - Egypt, Sudan, Burundi and the Democratic Republic of the Congo - one year to join the pact.
The new deal would need at least six signatories to come into force.
Burundi and the Democratic Republic of the Congo have not signed the deal yet and have so far been tight-lipped about whether they plan to or not.
Responding to the developments, Kamal Ali Mohamed, Sudan's water minister, said his country would now stop co-operating with the NBI because the agreement raised legal issues.
"We are freezing activities regarding the NBI until these issues, these legal implications, are resolved," he said.
Mohamed's statement drew expected criticism from Asfaw, who said the Sudanese had not revealed their intention to freeze co-operation during the two-day meeting.
Separately, Mohamed Nasreddin Allam, Egypt's water resources and irrigation minister, told the Reuters news agency that a meeting to discuss the Nile agreement would be held in Nairobi, the Kenyan capital, some time between September and November.
"The deal can not be forced upon us. It will only be an obligation for those countries, not Egypt's," he said.
"Ask the Egyptians to leave their culture and go and live in the desert because [you] need to take this water and to add it to other countries? No.
"Egypt has no source of water other than that coming from upstream countries. The upstream countries have many sources and aren't managing our Nile properly. That's what we are asking for."
Vital water source
Mena, the official Egyptian news agency, said on Monday that other states had said they "understood Egypt and Sudan's position ... and based on this an exceptional ministerial ... will be held to decide how to move forward in a matter that serves all Nile Basin states".
Stretching more than 6,600km from Lake Victoria to the Mediterranean, the Nile is a vital water and energy source for the nine countries through which it flows.
Egypt is almost totally dependent on the Nile and already threatened by climate change, is closely watching hydroelectric dam construction in East Africa.
Under the original pact Egypt, which faces possible water shortages by 2017, is entitled to 55.5 billion cubic metres a year - the lion's share of the Nile's total flow of around 84 billion cubic metres.
Around 85 per cent of the Nile's waters originate from Ethiopia and the Lake Basin is estimated to harbour more than half of Kenya's surface water resources.