* Bomb killed 21 people in popular Abuja shopping district
* Jonathan has been criticised for slow response to crisis
* President cut short African Union summit visit (Adds Nigerian ambassador to the U.N., paragraphs 13-16)
By Felix Onuah
ABUJA, June 27 (Reuters) - - President Goodluck Jonathan said on Friday Nigeria had entered one of the darkest phases of its history, visiting the scene of a bomb blast that had killed 21 people in an upmarket district of the capital Abuja two days earlier.
His sombre tone as he paid respects at the scene of the rush hour attack on a crowded central shopping district contrasted sharply with his tendency over the years to brush off the Boko Haram insurgency as a passing phase affecting only part of Africa's biggest economy and brightest investment prospect.
"This is one of the darkest phases in the history of our nation but surely we will get over it," Jonathan said in front of the cordoned area, still littered by rubble and charred cars.
"It is extremely painful that when some Nigerians are ... working hard to take care of their families and train their children, others are busy planning to kill people, intimidate."
Wednesday's bomb attack was the third on the capital since April, but the other two - car bombings of a bus station and street both in the suburb of Nyanya that killed about 90 people between them - did not strike at the heart of the city.
On Sunday, Jonathan told a delegation of African bishops that Boko Haram was "even worse than the civil war" against Biafran secessionists that killed a million people In the 1960s.
"In a civil war you know the battle line ... you know where to run to. But this one, the enemies are in your pocket."
Boko Haram, whose name means "Western education is sinful" and whose insurgency has killed thousands since 2009, made world headlines when it abducted 200 schoolgirls on April 14. Authorities have accepted help from Western powers to try to free them but any rescue would endanger the girls.
Jonathan cut short a trip to an African Union summit in Equatorial Guinea for the visit to the bomb site, highlighting how the insurgency may disrupt Nigeria's heavyweight regional influence.
Abuja's Wuse II district is popular with expatriates and elite Nigerians, although major embassies have not responded by updating travel warnings. A security source said that was because the plaza itself was still mostly frequented by locals.
The military said on Friday that two suspects arrested at the scene were being interrogated. They had shot dead another who had tried to escape on a motorbike and recovered a bag from him containing explosives, defence spokesman Major-General Chris Olukolade said in a statement.
Jonathan has in the past two months blamed the north's worsening security woes on global jihadist movements, calling Boko Haram "al Qaeda in West Africa," although many analysts see this more as a plea for help than a realistic view.
Nigerian ambassador to the United Nations Humphrey Orjiako read a speech on Friday in which he reiterated this position.
"Boko Haram is closely affiliated with al-Qaeda in the Maghreb, Al-Shabaab in Somalia, and other such radical extremist organizations in the Middle East," he said.
He added that Nigeria needs "collaboration beyond the African continent for sharing of intelligence on funding, sponsorship, incitement, access to weapons, equipment and other resources that facilitate the operations of Boko Haram."
A spate of deadly bombings outside of its northeastern heartlands - in Jos, Kano and Abuja - suggests Boko Haram is trying to push its sphere of influence outwards across Africa's top oil producer, security analysts say.
Jonathan's administration has been bruised by criticism of its failure to contain the insurgency or protect civilians, especially in the volatile northeast, but argues that Boko Haram's hit and run tactics make it hard to defeat. (Writing and additional reporting by Tim Cocks; editing by Ralph Boulton)