"I strongly believe all Nile Basin countries will sign the agreement."
The upstream countries want to be able to implement irrigation and hydro-power projects in consultation with Egypt and Sudan, but without Egypt being able to exercise the veto power it was given by a 1929 colonial-era treaty with Britain.
"We regret the intentional and announced absence of our dear brothers from Egypt and Sudan," Stanislas Kamanzi, Rwanda's water and lands minister, said.
The minister's comments came almost a week after Ahmed Abul Gheit, the Egyptian foreign minister, warned that Cairo's water rights were a "red line" and threatened legal action if a unilateral deal was reached.
The new agreement, the Nile Basin Co-operative Framework, is to replace a 1959 accord between Egypt and Sudan that gave them control of more than 90 per cent of the water flow.
The two countries have expressed fears that their water supply would be severely reduced if the seven other Nile users divert the river with domestic irrigation and hydro-power projects.
The Nile Basin Initiative, which had been spearheading the talks, will now become the Nile Basin Commission and will receive, review and approve or reject projects related to Africa's longest river.
The commission will be based in Addis Ababa, Ethiopia's capital, and have representation from all nine Nile Basin countries.
On Thursday, a senior EU envoy urged seven east African countries not to sign the new deal and settle differences with Egypt and Sudan first.
Marc Franco, who heads the European Union delegation in Egypt, said a separate deal would "make the political problems that exist worse".
The 1959 agreement allowed Egypt 55.5 billion cubic metres and Sudan 18.5 billion cubic metres of water each year.