French General François Lecointre, speaking after an initial fact-finding trip to Mali, where troops are fighting with French help to push back Islamist rebels who occupied the north of the country, said the army there was in a "very broken-down" state.
"It has been under-equipped, badly paid, badly trained and it is an army which has just suffered a full year of successive defeats which has considerably weakened it. There is a true moral strength to be rebuilt," he said in Brussels.
The EU has approved a 15-month mission to train Malian soldiers but Lecointre said a longer-term commitment may be needed to reconstruct the army.
French forces intervened this month after Mali appealed to Paris for urgent military aid to halt advances by the Islamists and defuse the risk of Mali being used as a springboard for jihadist attacks in the wider region or Europe.
"Recent events have highlighted that what might have seemed at the start like a short-term training mission of the Malian army is really a fundamental, absolutely necessary action for an army which collapsed very quickly in the face of the Tuareg offensive," Lecointre said.
Mutinous soldiers seized power from Mali's then president in a coup in March, angry at the government's failure to stamp out what was then a two-month-old separatist rebellion by the Tuaregs and eventually became the Islamist takeover that the army was powerless to halt after civilian rule was restored.
Dealing with Islamist desert insurgents
France has sent around 3,000 troops to Mali but is anxious not to get bogged down in a messy counter-insurgency war in their former Sahel colony.
The French have also made clear that while the first phase of liberating the biggest north Mali towns may be over, a more difficult challenge to flush the Islamist desert insurgents from their isolated rural lairs remains.
The crisis led the EU to bring forward its previously planned training mission by a few weeks.
The first European experts, who will advise Malian officers, will start work soon but the full force of about 250 trainers plus about 200 other soldiers to guard and lead the team will only be ready to start the training around the end of March.
Spain, Germany, Britain, Sweden and Ireland are expected to take part in the French-led EU training mission and non-EU members Norway and Canada may also participate, Lecointre said, but he gave no numbers for how many trainers each country would provide.
The EU's plan is to train four battalions of the Malian army, each with about 650 soldiers. Britain said earlier it had offered up to 40 soldiers for the training mission.
The Malian army also urgently needs help with equipment, Lecointre said, adding that until a few months ago, not every soldier had a gun.