"There have recently been reports of US helicopter raids in Hawija and Kirkuk. As Defense Minister Obaidi and numerous other Iraqi officials have stated, reports of these raids are untrue," Stuart Jones said in a statement on Saturday.
Recent reports of more than a dozen air raids led by US special forces have been decried by powerful Iranian-backed Shi'ite militias and other critics of Prime Minister Haider al-Abadi as violations of Iraqi sovereignty.
"I want to stress what I have said many times before: Iraqi sovereignty is sacred and must be respected. All coalition activities conducted in Iraq are and will be in consultation with the Iraqi government," Jones said, referring to the US-led coalition bombing ISIS targets and training Iraqi forces.
Iraqi parliament speaker Salim al-Jabouri told Reuters on Thursday foreign special forces have been conducting raids behind ISIS lines in Hawija ahead of an offensive planned later this year to retake Mosul, the largest city under ISIS control.
He said the raids were carried out "from time to time" and "supported by Iraqi forces" but did not specify whether the United States had played a role or how many had occurred.
Dubai-based al-Hadath TV and Iraqi media have reported several air raids over the last month in and around Hawija, 210 km (130 miles) north of Baghdad.
Washington said last month it was deploying a new force of around 100 special operations troops to Iraq to carry out strikes against ISIS there and in neighbouring Syria. US officials gave no details.
Both the US and Iraqi military have denied that US forces have carried out military operations on the ground in Hawija since October, when US special forces and Kurdish peshmerga commandos rescued 69 Iraqis in a raid in which one US commando was killed.