Soon after the signing ceremony, the two sides expressed disagreement over the Sanaa declaration's meaning.
Critics said the deal appears to have little substance, with Fatah and hamas agreeing only to open talks on a number of issues.
Further differences in interpretations emerged on Monday between advisers of Mahmoud Abbas, the Palestinian president, and al-Ahmed, who currently heads the Fatah parliamentary bloc at the Palestinian Legislative Council.
Nimr Hammad, a political adviser to Abbas, accused al-Ahmed of keeping the Palestinian president's office in the dark on the declaration's contents before signing it.
But al-Ahmed told Al Jazeera that he approved the agreement in co-ordination with Abbas' office, and denied that he had exceeded his brief.
Several policy positions and statements of intents were announced by Fatah and Hamas on Sunday after the signing of the Sanaa accord.
Interviewed by Al Jazeera on Monday, Ghazi Hamad, a spokesman for Hamas, said: "If you want to talk about implementation, I think you need more discussion and details. It's not easy to come the next day and say 'OK, let us start the implementation and return to normal life'.
"[But] if I suggest that Hamas cease control of Gaza, ... who will come and control the situation? Who will arrange the return of security forces? Who will be the head?
"There are many leaders of Fatah who became dissatisfied with the situation before 14 June – they complained that there was chaos and corruption."
Hailing the reconciliation deal, Abu Bakr al-Qurbi, the Yemeni foreign minister, said on Sunday: "Hamas and Fatah have agreed to accept the Yemeni initiative as a framework for dialogue ... and a return of the Palestinian situation to what it was before the events in Gaza [last June]."
He said the initiative would also "reconfirm the unity of the Palestinian homeland in terms of its land, people and the Palestinian Authority".
The deal calls for the restructuring of Palestinian security institutions, with the armed forces expected to come under the control of the Fatah-led Palestinian Authority (PA), rather than be loyal to any faction.
Yemen's peace initiative proposes seven points for Palestinian reconciliation
• Gaza must be returned to how it was prior to the Hamas takeover last June
• Agreement to hold early elections
• Resumption of dialogue on the basis of the 2005 Cairo agreement and the Mecca agreement of 2007
• Respecting the Palestinian Law and Basic Law and adherence to it by all parties
• Reconstruction of the Palestinian security institutions
• All Palestinian institutions to be free of any factional discrimination, subject to the law and the executive authorities
The two sides also agreed to adhere to previous commitments, including those made by Palestinian factions in Cairo in 2005 and the Saudi-sponsored Mecca accord between Hamas and Fatah that led to the formation of a short-lived Palestinian unity government earlier last year.
One of the sticking points of the deal, however, is a return to the status quo before June 13 in both the Palestinian territories.
The PA insists that implementation of the accord by Hamas is not open to negotiation.
"Resumption of dialogue [with Hamas] in the future must be to implement the Yemeni initiative in all its items and not to deal with the initiative as a framework for dialogue, because this will not yield an outcome," the PA said in a statement issued after the signing on Sunday.
Nabil Abu Rudeineh, another Abbas adviser, said: "The items of the Yemeni initiative are clear and we want it for implementation, not dialogue."
Hamas, on the other hand, says the agreement is a guideline for reconciliation talks, not a pre-condition.
Abu Marzouk told Al Jazeera: "There are two things [that are] very important - that we are going to return to a normal situation in Gaza and the West Bank, [and] the second one, that we consider the sticking points in the Yemeni initiative as the agenda of the negotiations."
Fatah says the agreement stipulates that Hamas must return control of Gaza to the PA, but has so far shown unwillingness to make changes in the West Bank.