Kenya and Rwanda have signed the Economic Partnership Agreement (EPA) with the European Union even as two of its EAC partners say the deal does not auger well for the region's economies.

The move, which comes hardly four months after the East African Community Council of Ministers agreed to have the member states sign the trade deal, is seen to likely cajole other EAC countries beat the September 30 deadline.

Being a single customs territory, however, the other EAC members – Tanzania, Uganda, Burundi and South Sudan must also sign the pact to make it enforceable.

Rwanda's Ambassador to Belgium Olivier Nduhungirehe posted pictures of Rwandan Trade minister Francois Kanimba and his Kenyan counterpart Adan Mohamed signing the agreements in Brussels Thursday on his Twitter account.

"#Kenya&#Rwanda, who signed the #EPA with the EU this morning, are the firsts @jumuiya partner states to sign," he said in the tweet.

The EPA is intended to guarantee the EAC traders duty-and-quota free access to the EU market in exchange for a gradual opening of up to 80 per cent of the region’s market to European products.

Kenya was desperate to have the agreement signed to safeguard unlimited duty free access of its exports to Europe after Tanzania and Uganda said the deal initialled in October 2014 needed to be renegotiated following Britain’s exit from the bloc.

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Kenya’s Industrialisation minister Mr Mohamed had on August 31 made an appearance at the EU Parliament as MPs discussed bid to lock out Kenya from its market from October 1 if the region fails to sign the EPAs.

In a statement, Mr Mohamed said he made a “concerted presentation” to the EU Parliament’s International Trade Committee (INTA) “and assured them of the EAC Partner States commitment to the EPAs.”

All EAC members have been negotiating the EPAs since 2007 leading to conclusion of negotiations in 2014 where it was initialled, translated and legal scrubbing concluded. Of the six members, Tanzania has publicly indicated its unwillingness to sign the agreement with Europe saying it could stifle its economy, while Burundi has been blowing hot and cold on the agreement.

Bujumbura has been wanting the signing to be tied to the sanctions EU imposed on the country last year following the political crisis caused by President Pierre Nkurunziza’s running for a controversial third term.

If the EPA is not signed and ratified by all EAC partner states by September 30, 2016, Kenya – being the bloc’s only developing state - stands to lose its market to the EU, having significant impact on her economy.

The rest of the members have alternative access to EU as they are all classified as least developed countries.