The Joint Implementation Committee (JIC) established by the agreement was to review and assess its application. The committee, chaired by ECOWAS, was to meet at least once every three months and include members of the Commission for the Consolidation of Peace (CCP), regional diplomatic representatives and officials of the agreement's 'moral guarantors' – Togo, the UN, the OAU and the Commonwealth. However, the agreement did not spell out how the JIC was to relate to other institutions established under the agreement, such as the CCP or the Council of Elders.
Military problems began to appear soon after the signing. The role of ECOMOG, the West African peacekeeping force, needed to be reviewed in light of the transformation of the mandate of the United Nations Observer Mission (UNOMSIL) to peacekeeping status (UNAMSIL). Pressures on the Nigerian political leadership to remove their majority contingent in ECOMOG led to the decision to pull out. The option of two separate entities under separate commands in the same theatre of military operations was not seen as being viable. The UN, for policy reasons, refused to give financial support to a regionally constituted force. The compromise adopted was to phase out ECOMOG and absorb part of it into UNAMSIL. This changeover presented an opportunity for those wanting to test both the capabilities and resolve of the newcomers.
The tense and ambiguous situation in the country that brought the conflict parties back to the battlefield in May 2000 was ignited by confrontation between the RUF and UNAMSIL, climaxing in 500 peacekeepers being taken hostage by the RUF forces. From the start, the RUF contested the legitimacy of UNAMSIL and then obstructed its operations. Even before the hostage-taking incident, the RUF had demonstrated its rejection of the UN peacekeepers by seizing large quantities of arms, ammunition and heavy military equipment in two separate incidents. According to Oluyemi Adeniji, special representative of the UN secretary general in Sierra Leone:
"From its induction in Sierra Leone, Sankoh had displayed an antagonism which proved implacable to the UN Mission UNAMSIL. He denounced its deployment as illegal and inconsistent with the Lomé Agreement, done without his agreement and threatening to his party. Every effort made to explain the link between UNAMSIL and article XVI of the Lomé Agreement met with a pretence at understanding, only for UNAMSIL to be denounced again shortly thereafter. With that posture, RUF obstructed UNAMSIL from deployment throughout the country, protection of innocent Sierra Leoneans and others from gross violation of their human rights and assisting the extension of the authority of the Government of National Unity throughout the entire country." (Report to 3rd JIC meeting, 13 May 2000)
At the political level, the JIC appeared to have little effect in mediating disputes arising from the agreement. At the second committee meeting, held on 24 January 2000, the RUF representative Solomon Rogers suggested that during the life of the current government and until general and presidential elections, the Lomé Agreement should take precedence over the constitution. Rogers' contention was summarily dismissed on the grounds that the Lomé document's section on 'governance' situated the agreement squarely 'within the spirit and letter of the constitution'. However, rejecting the RUF position conveniently ignored the fact that, in one area at least, the designers of the Lomé Agreement had been obliged to bend the constitution. In their effort to carve out a niche within the country's power structure for the RUF, they had offered Sankoh a 'status equivalent to vice president', even though only one vice president is provided for in the constitution. This political surgery, done in the name of peace, was apparently perceived by Sankoh as the opening of a dam of privileges and powers for him. When this did not happen, he constantly complained, as he once did to parliament, that his VP status was just a 'white elephant'.
Some of the other major problems were related to the inclusion of the RUF in the Government of National Unity, the RUF's establishment as a political party and the setting up of key structures created by the agreement. On several occasions, including the last press conference called by Sankoh before he fled into temporary hiding on 8 May, the RUF reiterated their claim that the government had not honoured its commitment to offer the RUF Party all the political, diplomatic and para-statal posts provided for in the agreement. The agreement had reserved for the RUF 'one of the senior cabinet appointments such as finance, foreign affairs or justice' and not one of these was offered. Instead, the government conceded the ministries of trade and industry, and of energy and power. It leaned on the semantic argument that the expression 'such as' should not mean 'that is' and it could therefore designate any posts considered to be of the same standing as those indicated.
The real bone of contention, however, was to become the allocation of diplomatic and para-statal jobs. The government claimed that it had decided to privatise the para-statals due to their poor management and that it was unnecessary to make fresh appointments to their boards. As far as diplomatic appointments were concerned, one can only interpret the eagerness of the RUF to get these posts as the expression of a desire to test their international 'acceptability', taking into account that the blanket amnesty granted by the Lomé Agreement was not fully endorsed by the international community. One surprising aspect of the tussle was that some cabinet members dismissed as a trivial detail what the RUF considered to be of crucial importance. Government claims of insufficient funds to set up diplomatic missions due to the continued occupation by the RUF of the country's revenue base – the diamond-rich district of Kono – were contradicted by the appointment of new ambassadors to Libya and Ghana.