Tunisian President Kais Saied has rejected financial support announced by the EU in September, saying the “small amount” goes against a deal signed three months ago.
Mr Saied's move could undermine the “strategic partnership” from July that includes measures on combatting human traffickers and tightening borders.
The deal was agreed during a sharp increase in boats heading to Europe from the North African nation.
About €100 million of that amount was expected to go towards helping Tunisia secure its borders.
“Tunisia rejects what the EU announced, not because of the small amount, but because the proposal conflicts with the memorandum of understanding signed in July,” Mr Saied said.
The July deal included a pledge of €1 billion in aid to Tunisia to help its battered economy, rescue state finances and deal with the migration crisis.
The smaller amount announced by Europe 10 days ago, however, has frustrated Tunisian authorities struggling to improve public finances and raised fears among credit rating agencies that the government could soon default on foreign debts.
The dispute between the two parties has coincided with the arrival of record numbers of migrants from Tunisia and North Africa to the Italian island of Lampedusa.
Last week, Tunisia postponed a visit by a delegation from the European Commission to discuss the details of the migration agreement.
In September, it denied the entry of five members of the European Parliament’s foreign affairs committee for meetings over the political situation in Tunisia, saying it would not allow interference in its affairs.
Some European countries, including Germany, oppose the immigration deal, saying it does not address human rights issues and the political situation after Mr Saied seized power, shut down the Tunisian parliament and began ruling by decree in what the opposition says was a coup.