After months of positive progress, the two and a half-year-old peace process in Colombia between the government and rebel group the Revolutionary Armed Forces of Colombia (FARC) is in crisis once again.

A brazen ambush by the rebels on a military patrol that left 11 soldiers dead and another 20 injured in the Cauca region has caused the current predicament.

The attack was the deadliest since the sides started negotiating in Havana, Cuba and it appears to be a blatant violation of the rebels' four-month-old unilateral ceasefire.

It left President Juan Manuel Santos with no option but to resume air raids against the FARC camps, which he had temporary suspended as a gesture of goodwill after the rebels had shown to have respected their side of the deal.

Santos's goodwill expired on Tuesday night, when FARC rebels hit the army patrol with all they had: explosives, grenades and firearms.

The public outcry has been strong and rightly so. The intensity of the combat and the disparity in the number of victims (just one dead among the rebels) has destroyed the little confidence a wary public had about FARC's willingness to pursue peace.

Political opponents, such as the former president, Alvaro Uribe, have been quick to accuse the government of going too soft on the rebels and being manipulated by guerrillas.

But the truth is that incidents like this are almost inevitable unless there are fundamental changes in the situation on the ground.

The not-so-complete truce

While the attack was particularly brutal, it is unsurprising given that the sides are negotiating as the conflict continues.

It is true that there has been some progress in de-escalating the war, however the rebels continue their activities in many regions of the country.

So does the army. In some cases, it has increased its activity on the ground, pursuing the drugs trade and illegal mining, two of the ways through which the rebels finance their activities.

General Mario Augusto Valencia, the commander of the third division of the Colombian Army, said his men had been operating in the area where the attack occurred for more than two months.

“We have been carrying out territorial control missions to protect the local civil population but we’ve also been attacking the criminal activity in the area; drug trafficking, extortions," Valencia said.

The Cauca region where FARC rebels attacked the soldiers is known for drug-trafficking and explosives smuggling [Al Jazeera]

"There's a region where a guerrilla group, FARC mobile column (branch) Miller Perdomo, (that has) a particular squad directed by alias Chichico, a narcoterrorist that runs drug-trafficking in the area and explosives.

"And we hit them hard, just this year we have confiscated supplies they had worth over 7,000 million pesos ($3m). We’ve destroyed their explosives labs and drug labs,” Valencia said.

The Cauca region is a major drugs and weapons corridor to the Pacific. And even with the ceasefire in place the rebels will not let their businesses be disrupted without fighting back. So Tuesday’s attack was most likely an act of retaliation by the local FARC branch.

Some believe the FARC negotiators in Havana might have tried to use the ambush to pressure the government into a full bilateral agreement, but it seems dubious. If anything the attack shows just how complicated and volatile the reality of the war is in many regions and how difficult it is for FARC commanders to control and prevent their troops from reacting to renewed military action.

Keeping it cool

This reality is difficult to accept for many Colombians rightly angered and tired of the violence and of actions that contradict the gains at the negotiating table.

President Santos might be tempted by a major offensive to calm an angry military and public opinion but that would also prompt retaliation by the rebels. He could also decide to issue a deadline for the talks. Both choices would likely just increase the risk of failure.

The good news is that both sides have invested all of their political capital in the process and are still committed to reaching a full agreement.

Most analyst think it is unlikely that this crisis will lead to collapse of the negotiations.

“It’s one of the most difficult moments in the entire negotiations process," said Markus Shultze-Kraft, a conflict analyst at the Icesi University in Cali.

"However I would say it is above all a big political issue. It’s not a military issue, it’s not a security issue, it’s a political issue, and as such it should be dealt with politically," he said.

"By that I mean for dialogue and transparency on what has happened, why did this happen, who was involved and how can the issue be resolved through dialogue in order to buttress the negotiation process in Havana.”