Egypt has limited its participation in the Nile Basin Initiative since 2010 when Rwanda, Ethiopia, Uganda and Tanzania signed a new treaty on equitable sharing of Nile waters.
Burundi and Kenya later also inked the deal which stripped Egypt of its power to veto upstream irrigation and hydropower projects.
The Cooperative Framework Agreement replaced a decades-old pact that gave Egypt and Sudan rights over more than 90 percent of the Nile's waters.
Egypt is almost entirely dependent on water from the Nile.
To protest the 2010 pact, Cairo withdrew from the Nile Basin Initiative (NBI), a forum for riparian countries to discuss joint management and development of the region's resources.
"I should like to place an appeal to our sister nation Egypt. Please, your seat is still empty," Sudan's water resources and electricity minister, Muattaz Musa Abdallah Salim, said at the annual meeting of Nile Basin water ministers.
"Your resumption of your activities in NBI will further consolidate our gains and integrity in the region," Salim said.
Egypt did send a delegation to the Khartoum talks because they are a chance to discuss the controversial Framework Agreement, Ahmed Abu Zeid, counsellor with Egypt's foreign ministry, told AFP on the sidelines of the talks.
But except for such ministerial meetings Cairo has not participated in any other NBI programmes or bodies since 2010, he said.
Egypt's new water resources and irrigation minister, Hussein Mohamed al-Mughazi, was not part of the Cairo delegation because he was only sworn in on Tuesday, Abu Zeid said.
"We thought that the logic and the rules of procedure say that any agreement should be by consensus on all the articles, which didn't happen. So we had to freeze our membership since then," Abu Zeid said.
He said there have recently been encouraging statements from some signatories to the Framework Agreement. They indicated there is a need "to re-encourage the dialogue again amongst all the countries".
In a speech to the forum, Jemma Nunu Kumba, South Sudan's water minister, reiterated "the need to continuously engage Egypt both formally and informally".
Kumba is the outgoing chairwoman of the ministerial group.
Sudan also froze its NBI participation after the 2010 treaty but resumed involvement last year.
Egypt has expressed particular fears that Ethiopia's 6,000 MW Grand Renaissance dam project could diminish its water supply.
The dam will be Africa's largest when completed in 2017.
Cairo raised its concerns in three-way talks between Egypt, Ethiopia and Sudan, but they have not met since January.
There is no schedule but we always invite them to come to the discussion," Ethiopia's water minister Alemayehu Tegenu told AFP, adding that construction of the dam is going well.
Abu Zeid said Egypt hopes for "common ground to start a constructive dialogue" on the Ethiopian hydro project.
The 6,700-kilometre (4,154 miles) Nile River is one of the world's longest and drains about 10 percent of Africa.
NBI says its cooperative mechanism has brought tangible benefits, including a cross-border electricity link opened in December between Sudan and Ethiopia.
Democratic Republic of Congo is NBI's 10th member.