Presdindent Salva Kiir has come out to defend why he accepted the 100 days extension, saying this was meant to avoid South Sudan from returning to war.
"I, as your president had to accept the 100 days extension to avoid the potential for SPLM/A-IO to have a reason to return the country to war again. Honestly, I accepted it because the government didn't honour the pledge to pay the remaining part of the $100 million to National Pre-Transitional Committee for the implementation of the agreement," President Kiir told journalists at Juba International Airport.
However, the deputy co-chair of the National Pre-Transition Committee (NPTC) Gabriel Changson said the government recently paid $40 million out of the $100 million it pledged last year.
The parties to the peace deal had for a long time not agreed the implementation of security arrangements including the unification of forces, cantonment and settling of issues in regards to number and boundaries of states.
But at the Entebbe meeting called by Uganda's President Yoweri Kiguta and Sudan's head of Sovereign Council Abdel Fattah Al-Burhan, President Kiir and opposition leader Riek Machar agreed for the second time extension of pre-interim period to allow full implementation of the security arrangements.
The new pre-transitional period will start on November 12 to February 22, 2020.
Political analysts from think-tank Sudd Institute and peace campaign groups had warned that Dr Machar's faction was likely to use violence if President Kiir excluded him from the unity government.
President Kiir has also been accused of lacking political will to release funds for the implementation of the key provisions, including training and unification of the necessary force.
Earlier, secretary general of South Sudan Council of Churches had called on political leaders to reflect on the pledges they made after the Rome spiritual retreat in Vatican early this year.
In April this year, South Sudan Council of Churches in partnership with the Vatican organised a spiritual retreat that brought together President Salva Kiir, First Vice President designate Machar, First Vice President Taban Deng and Rebecca Nyandeng. The group travelled to Rome for a meeting with Pope Francis and discussed the country's peace-building process.
In an interview with The EastAfrican, Father James Oyet called on the political leaders to reflect the pledges they made in Rome, saying the pledges will only bear fruit if the two factions formed an all inclusive coalition government that will deliver services to the people of South Sudan.
The secretary general added that those pledges cannot be achieved if the political leaders don't meet regularly inside South Sudan to dialogue on issues to do with the revitalised peace accord, formation of Transitional Government of National Unity.
"They pledged publicly to work for peace for the people South Sudan, you cannot work for peace when far away, you need to be closer to each other so that you can discuss your issues that disturbs you. You cannot talk through media or social media with your brother, why don't you reach him face-to-face as Pope told them" said Father Oyet.
At the Vatican retreat, Pope Francis expressed his wish to ascertain the conditions for a possible visit to South Sudan as a sign of closeness to the population and of encouragement for the peace process. The Pope knelt before leaders and wiped their feet.
The political leaders vowed publicly to work for the common interest of the citizens particularly implementing the revitalised peace agreement.
Jame Kolok, the executive director of Foundation for Development and Accountable Governance said the actions of the leaders after the Rome visit didn't meet the citizens' expectations.
"We thought that by meeting the Pope, the politicians would change their minds and swiftly move forward ensuring that they revise from the suffering of the local people, that didn't happen, we still see a lot of challenges in terms of the implementation of the peace agreement, we see a lot of laxity in financing this process and generally we see a complete laxity of political will to ensure that South Sudan achieve durable peace and stability" said Jame Kolok.