Impeached Ekiti State Governor Ayo Fayose went into hiding
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Nigerian senators have warned President Olusegun Obasanjo they should be consulted before any future state of emergency declarations.
But they voted to approve the appointment of a former general to run the south western state of Ekiti.
The president acted after impeachment moves in Ekiti ended in a legal row.
Opposition politicians argued the move was unnecessary and part of a wider plan by Mr Obasanjo to consolidate his control in the run-up to April polls.
Two other governors are currently involved in contentious impeachment proceedings.
The assembly debate was seen as a test of the president's authority ahead of the elections, which should mark the first civilian transition in Nigeria's history, with Mr Obasanjo standing down after two terms in office.
After a meeting lasting late into the evening, the Senate finally endorsed the action, but added a resolution that in the future declarations of an emergency should be discussed with the National Assembly first.
The BBC's Alex Last in Lagos says the whole episode was an indication of how much disquiet the declaration has created, with elections just round the corner.
Nigeria's constituent states and their leaders play a major role in determining who will be the president's successor.
The state of emergency in Ekiti was imposed after the impeachment of the state governor was declared unconstitutional.
In the ensuing political chaos, several different politicians declared themselves to be the rightful governor.
The president then stepped in and appointed a former general and political ally to administer the state.