Julia Price, who owns the building, said she had received after receiving a call from Telford & Wrekin Council telling her the building may have to be repainted again.
The council says it is currently investigating the paint job after receiving complaints from members of the public.
Mrs Price and her husband Gary, whose company carried out the makeover, had decided to change the building from its original cream colour to help brighten up Newport's High Street.
She said several people had told them they loved the new look and hundreds of people have backed her on Facebook since the council announced its ruling.
Mrs Price said the work had cost £1,296 and that a similar sum would be needed to paint the building again.
Mrs Price, said: "We were really upset when we got the call off the council telling us we need to repaint the building.
"Its only been the lilac colour for a week and so many people have told us how much they love it.
"I even had one lady who lives in Market Drayton say she went the long way home just so she could see the new building.
"When me and my husband bought the building 14 years ago we were told that we could repaint the front, and that any pastel colour was fine.
"But I guess some people just don't agree with us. Looking down the High Street there are so many different coloured buildings so I don't understand what is so bad with ours."
The building dates back to the 1400s and since the couple took over it in 2001 they have renovated the building to make it more modern.
Boughey House was also one of the only buildings to survive the Great Fire of Newport in 1665.
"It has a total of five floors," Mrs Price said. "And we have three floors which are in use by our clients.
"Everyone who works in the building is self employed, they rent different rooms and run businesses from here, mainly beauty rooms and hair salons.
"They all seem to have given positive feedback about the colour and so have many of their clients.
"I just don't understand why some people don't like the building when pretty much all the feedback has been very positive."
Russell Griffin, spokesman for Telford & Wrekin Council, said: "We are aware of local residents' concerns relating to work that has been carried out at Boughey House in Newport High Street.
"We are currently investigating this issue in relation to the relevant planning acts.
"However it may well be that we invite the owner to submit an application for retrospective listed building consent – although that does not presume that such an application will be approved.
"If officers feel that the work is inappropriate and has damaged the character of the listed building, an option open to the council is to serve a listed building enforcement notice."
Anyone wishing alter or extend a listed building in a way that affects its character or appearance as a building of special architectural or historic interest – or even demolish it – must first apply for listed building consent from their local planning authority.
A planning authority can insist that all work carried out without consent is reversed, and Historic England advises people to always talk to their local planning authority before any work is carried out to a listed building.