“They’re everywhere,” said the Iraqi intelligence officer, sweeping his arm from this ancient Christian village toward the horizon. The Iraqi captain was searching for tunnels dug by Islamic State fighters.

The officer stomped on the ground. “Here. We found one, then three, now six. Right here.” And over there? “More,” he said. “And more.”

Villages recaptured from ISIS over the past three weeks by the Kurdish peshmerga and Iraqi army forces on the road to Mosul have been honeycombed with tunnels, many of them booby-trapped.

In the past three days, commanders say Iraqi forces have faced the hardest fighting of the offensive as they entered Mosul, made worse by extensive tunnels that are allowing ISIS fighters to appear seemingly out of nowhere, attack, then retreat to the hidden bunkers.

“The clashes have been very, very violent,” especially on Friday and Saturday, as troops advanced deeper into the city held by ISIS for the past two years, said Brig. Gen. Yahya Rasoul, a spokesman for the Iraqi military

“It’s house-to-house fighting now,” said Rasoul, who declined to give casualty figures.

With Iraqi special forces now battling for the eastern districts of Mosul, commanders say the omnipresent tunnels, alongside holes smashed between the walls of buildings, are allowing hidden ISIS fighters to move quickly into position to ambush advancing troops and then pivot to concealed locations.

An Iraqi armored commander who drove his Abrams tank into eastern Mosul recalled seeing dozens of fighters scrambling on the street in front of his guns.

“Then they disappeared,” he said. Into the ground.

“It’s like we are fighting two wars in two cities,” said Col. Falah Al-Obaidi of the Iraqi counterterror forces. “There’s the war on the streets and there is a whole city underground where they are hiding.”

The colonel complained, “Now it’s hard to consider an area liberated, because though we control the surface, ISIS will appear from under the ground, like rats.”

Obaidi and other commanders said that they knew urban warfare among civilians and human shields in Mosul would be difficult, but the tunnels are making it worse. The officers described the battlefield as more of a sphere than a plane — with threats coming from side to side, above and below.

Journalists embedded with Iraqi special forces reported ISIS fighters popping out of tunnels after areas were secured to fire at the troops.

The number of tunnels is unknown. ISIS fighters dug extensive tunnels under Fallujah, which was recaptured by Iraqi forces in June.

ISIS didn’t invent the tactic. Tunnels have been used in warfare for thousands of years, especially valued in asymmetric guerrilla war. Jewish rebels used tunnels against Roman legions; the Viet Cong did the same against U.S. troops in Southeast Asia.

Here in Karemlash, Iraqi Christian militias uncovered cramped earthen burrows used by ISIS fighters to hide from surveillance drones, artillery shells and U.S.-led airstrikes.

The tunnels were dug into a hill that covers an archaeological site for an ancient Assyrian city. The Islamic State also commandeered the Saint Barbara convent and dug deep tunnels through the floor of the chapel. The village marks the site where Alexander the Great fought the Persian emperor Darius in 331 B.C.

Some tunnels go for hundreds of yards. The earth is hard-packed and laced with rocks, and the passageways illuminated with electric lights.

In one set of tunnels in the village of Shaqouli there were subterranean dormitories, still littered with mattresses and blankets. Someone had decorated the rooms with flowered wallpaper and ISIS posters.

Iraqi troops have found weapon caches, small kitchens, food pantries and rooms stacked with explosives.

The floor of one tunnel was littered with onions, eggplants and spilled sugar. There were unwashed pots and pans with a residue of dried beans.

To conceal their digging from drones and satellites, ISIS usually hid the dirt. In the houses near tunnel entrances, rooms are filled from floor to ceiling with soil.

The longest tunnel discovered so far stretched for six miles at the edge of Mosul, according to Iraqi commanders, dug by Islamic State cadres with help from civilians probably forced to shovel.

The tunnelers employed drills originally designed for mining operations or the oil fields, the Iraqis said.

One large drill mounted on half-tracks was discovered in a tunnel outside of Judayda al Mufti at the edge of Mosul.

The Iraqi intelligence officer, who serves in the Iraqi 9th Armored Division but declined to have his name used because of his position, complained that because of booby traps, his men haven’t found all the entrances and exits of tunnels.

When they do find a suspicious hole, the troops toss grenades into the darkness, followed by flaming tires. They said they cannot be too sure that ISIS fighters don't return to surprise them.

Loveday Morris and Mustafa Salim in Erbil contributed to this report.