EU Commission President Ursula von der Leyen gives her annual State of the Union address during a plenary session at the European Parliament in Strasbourg, eastern France, on September 13, 2023. AFP
The Ombudsman, Emily O'Reilly, is an independent overseer employed to handle complaints about the work of EU institutions and agencies and to investigate alleged administrative failures.
"Where fundamental rights are not respected, there cannot be good administration," she said.
In July, the European Union signed a deal to provide financial assistance and practical cooperation to Tunisia -- the main launchpad for undocumented migrants making the dangerous sea crossing to Italy.
European Commission president Ursula von der Leyen, Italy's Prime Minister Giorgia Meloni and the Netherlands' Mark Rutte hailed the deal as a way to fight "networks of smugglers and traffickers".
But international human rights organisations and some MEPs have criticised Brussels for forming an anti-migration partnership with President Kais Saied's increasingly authoritarian regime.
In recent months hundreds of migrants arrested in Tunisia have allegedly been dropped off in the desert near the Libya border and left to fend for themselves.
Against this backdrop, O'Reilly said von der Leyen's European Commission has some explaining to do.
"Did the Commission carry out a human rights impact assessment of the MoU before its conclusion and consider possible measures to mitigate risks of human rights violations," the ombudsman asked, in a letter to von der Leyen.
"If yes, could the Commission make this impact assessment public, along with the mitigating measures? If not, please set out the rationale for this."
O'Reilly noted that she had raised these concerns when Brussels signed a similar pact with Turkey, and warned the EU regulations stipulate that any funding provided to partner countries must not be spent in ways that breach migrants' human rights.
"How does the Commission plan to ensure that actions undertaken by Tunisia under the Migration and mobility pillar of the MoU and financed using EU funds will comply with the applicable human rights standards?" she asked.
Earlier this week, the European Commission was forced to defend the Tunisian migration pact in parliament, where it has come under fire from MEPs from the left and the Greens.
"This is an investment in our shared prosperity, stability, and in the future generations," commissioner Oliver Varhelyi told the European Parliament in Strasbourg.
He said it reinforced cooperation that has already seen the Tunisian coast guard intercept nearly 24,000 boats headed for Europe this year, compared with some 9,000 last year.
But the row flared up again on Thursday when Tunisia barred entry to a fact-finding delegation from the European Parliament, following a non-binding resolution condemning the government's "authoritarian drift".