* Sri Lankan investigation, Iran visit urged
* Pillay calls on Egypt to stop killing migrants
* To discuss Italy's treatment of Roma, migrants next week
(Adds Sri Lanka reaction)
By Jonathan Lynn
GENEVA, March 4 (Reuters) - Human rights abuses in Sri Lanka are damaging prospects for reconciliation after 25 years of civil war and a violent crackdown on dissent in Iran is deeply worrying, the top U.N. human rights official said on Thursday.
Repeating her call for an independent investigation into war crimes allegations in Sri Lanka, U.N. High Commissioner for Human Rights Navi Pillay told the U.N.'s Human Rights Council she was singling out outstanding cases in different countries.
"I am convinced that Sri Lanka should undertake a full reckoning of the grave violations committed by all sides during the war, and that the international community can be helpful in this regard," she said in a speech presenting her annual report.
The opportunity for peace and reconciliation in Sri Lanka was marred by the treatment of journalists, human rights defenders and other critics of the government.
Her comments on Sri Lanka and other states will reassure critics of the council who argue that the 47-member body often fails to deal with human rights violations as countries unite in regional alliances to shield each other from scrutiny.
Last May, the council held a special session on Sri Lanka just after the end of the war against the Tamil Tigers, but the government deflected criticism by introducing its own resolution praising its defeat of the separatist group, which was then passed, boosting the Colombo stock exchange. [ID:nCOL24904]
Rajiva Wijesinghe, former secretary in the human rights ministry who has resigned to stand in April 8 parliamentary elections, rejected the charge of abuses linked to the war.
Pillay, a former U.N. war crimes judge, said she had talked with Iranian officials about the deteriorating human rights situation in Iran, which is seeking a seat on the council, and suggested her office should visit the country.
Demonstrators, rights activists, journalists and prominent politicians had received harsh sentences, including capital punishment, for their role in protests after the disputed election last year following questionable trials, she said.
Pillay said continuing executions in Sudan were deeply troubling, and she repeated her call for an independent inquiry into killings by Egyptian forces of unarmed migrants trying to enter Israel via the Sinai Desert. [ID:nLDE6210IF]
In a separate statement, Pillay condemned violence against women, especially an estimated 5,000 "honour killings" a year worldwide. These could not be brushed aside as a primitive atrocity happening elsewhere but were an extreme form of discrimination against women plaguing every country, she said.
Pillay dismissed the argument that family violence was outside international human rights, and said states had a clear duty under international law to uphold women's rights and ensure freedom from discrimination.
The South African jurist also directed comments against rich countries, saying the treatment of Roma in some European states, such as Slovakia and the Czech Republic, was deteriorating.
Pillay told the council she would raise the issue of discrimination and attacks against Roma and other migrants with the Italian authorities when she visits Italy next week.
The United States -- which joined the council last year after boycotting it under the previous administration of George W. Bush -- had made some progress in steps to close its prison in Guantanamo Bay and to ban illegal methods of interrogation and transfer of prisoners, she said.
"The United States should now conduct thorough investigations into allegations of torture at the detention centres in Guantanamo Bay and Bagram, account for practices that may have contravened international law, and hold violators to account," she said, referring to U.S.-run centres for security detainees in Cuba and Afghanistan. (For full Pillay speech go to link.reuters.com/naj33j ) (For annual report go to link.reuters.com/taj33j ) (Additional reporting by Shihar Aneez in Colombo) (Editing by Stephanie Nebehay and Elizabeth Fullerton)