They claimed that their cabin was bed-bug ridden and had dirty sheets.
Janice visited the on-board doctor for treatment, which led to the couple's cabin being fumigated twice, on doctors' orders, during their week.
The newlyweds, who are now suing Tui UK Ltd over the experience, told their lawyers that food on the ship was served under-cooked and lukewarm.
Janice allegedly suffered with diarrhoea, vomiting, chest and stomach pains while on board, which left her feeling so ill that she couldn't leave the ship for the excursions.
But her woes didn't end there, as Janice has developed chronic fatigue syndrome and has had to take voluntary redundancy from work since returning from their honeymoon.
Janice, 48, said: "This was supposed to be a fantastic way for us to spend our honeymoon but it simply didn't work out that way and I have been left with long-term health problems as a result that continue to impact my everyday life.
"The ship really wasn't up to the standard we expected and the illness I suffered was absolutely horrendous.
"The fact that it continues to affect me to this day has just added insult to injury for me."
The exact cause of Janice's chronic fatigue remains under investigation and may be as a result of a post viral infection, caught on board the ship, according to the couple.
She added: "We are determined to find out what caused my illness and to ensure that any changes that can be made on the ship are highlighted in the hope of preventing something similar happening to someone else."
The couple have instructed Irwin Mitchell to represent them and have already started legal proceedings against TUI UK Ltd.
They hope to find out what caused their illness and win compensation for the holiday and the long-term implications the illness has had on their lives.
So far, TUI UK Ltd have neither admitted nor denied liability.
Jennifer Downing, who is representing Philip and Janice, said: "Clearly this was supposed to be a relaxing and romantic trip for Janice and Philip but they were left unable to enjoy the facilities they had paid for due to the illness they experienced.
"We have been instructed by a number of people who suffered similar problems on board this ship at the same time Janice and Philip were on board, as well as passengers who travelled on the Thomson Celebration during other voyages in 2014 and 2015.
"Understandably, Philip and Janice want answers about the illness Janice suffered, which continues to affect her to this day, and to understand why their honeymoon cruise was ruined."
Irwin Mitchell has also been instructed to act on behalf of a number of other passengers who were also on board the cruise ship at the same time as the couple.
TUI UK Ltd could have multiple lawsuits on their hands as the firm have also been instructed by groups of passengers, who suffered illness on the same ship, during voyages in 2014 and 2015.
A Thomson spokesperson told MailOnline Travel: "We are sorry to hear of Mr and Mrs Stephens experience.
"As this is now subject to legal proceedings, it would be inappropriate for us to comment further.
"We closely audit all resorts to which we operate to ensure that health, hygiene and comfort levels are maintained in line with industry standards."
