One resident in flood-hit Stainforth in South Yorkshire told the Mr Johnson: "I'm not very happy about talking to you so, if you don't mind, I'll just mope on with what I'm doing."
The woman, clutching a wheelbarrow alongside the troops sent to the area to help, added: "You've not helped us up to press. I don't know what you're here today for."
Another told him: "You've took your time Boris, haven't you?", to which Mr Johnson replied: "We've been on it round the clock."
Speaking to reporters at the scene, Mr Johnson said: "I perfectly understand how people feel and you can understand the anguish a flood causes.
"The shock of seeing your property engulfed by water is huge and also the anxiety of what may still be to come and I do thank the emergency services for everything they are doing."
Mr Johnson arrived in the area as nearly 100 soldiers began assisting communities cut off by the flooding.
Personnel from the Light Dragoons laid down sandbags in Stainforth near Doncaster, attempting to shore up the village's bridge.
Another local, Shelly Beniston, told the Prime Minister she had helped organise supply runs to the neighbouring village of Fishlake, another area to be hit by flooding.
She said: "We've had no authorities helping us. We didn't know where to start. We just used common sense basically."
Another man shook the Prime Minister's hand and said: "Help these people out. They definitely need it. Well done Boris."
The help from the Army comes amid fears that further bad weather could be on the way on Thursday, with the Met Office issuing a yellow warning for rain for the whole day covering a vast region from Portsmouth to Hull.
One official from the Environment Agency told Mr Johnson that an estimated 20mm to 30mm of rain was expected to fall in the next 24 hours.
The official said that 2019 had already seen the third wettest autumn on record, adding: "We need to look at what we need - particularly in the context of a changing climate."
There are 34 flood warnings still in place across England, in locations from Somerset and East Sussex in the South, to as far north as the Lower River Nidd near Harrogate in Yorkshire, and the Holderness Drain in east Yorkshire.
Seven flood alerts are also in place in Wales, where the Met Office is predicting further heavy rain on Wednesday.
But five severe "danger to life" warnings on the River Don in South Yorkshire have been downgraded.
On Tuesday evening, the Prime Minister warned there could be further flooding across the country after chairing a meeting of the Government's emergency committee.
Mr Johnson also announced relief funding would be made available for those affected by the floods and said that funding for locals councils to help affected households would be made available to the tune of £500 per eligible household.
Up to £2,500 would be available for small to medium-sized businesses which have suffered severe impacts and which are not covered by insurance.
The PM also urged people in affected areas to heed the warnings of emergency services, after some residents in Fishlake remained in their homes despite being advised by Doncaster Council to evacuate.
The announcements came after both Labour and the Liberal Democrats criticised the Government's response to flooding, which is rapidly turning into an election issue.