Ecowas had called on Mr Tandja to postpone the vote indefinitely to allow talks with opposition politicians - who have boycotted Tuesday's election.
They are angry at the president's attempts to extend his time in power.
Mr Tandja dissolved parliament earlier this year and had the constitution changed to let him seek a third term.
After talks at the weekend, Ecowas had warned the 71-year-old president to delay the election or face "full sanctions".
On Tuesday the bloc's political director, Abdel Fatau Musa, told the BBC's Focus on Africa programme it was clear Mr Tandja had rejected the decision of Ecowas.
He defended the decision to suspend the nation, saying it would affect Mr Tandja.
"If you are considered a pariah, an outcast, from an organisation you have ratified the conditions of, then psychologically it will affect you," he said.
He warned that the issue could end up in the UN Security Council, and Niger could be left in international isolation unless Mr Tandja backed down.
The president's move to stay in power in the uranium-rich nation sparked international outrage and dismay among opposition groups.
He had been due to stand down in December after serving two five-year terms.
But his supporters say the people want him to stay in power because he has brought financial stability to one of the world's poorest nations.
In January, French company Areva signed a deal to develop what it said would become the world's second biggest uranium mine.
The mine is in the semi-desert north, where ethnic Tuareg rebels have been fighting for more autonomy.
President Tandja has signed a peace deal with several Tuareg groups.
Six million people are eligible to vote to elect a new 113-member parliament, but correspondents say the campaign has been marked by indifference among residents.
SOURCE: BBC News