The PSNI said a gang forced entry into the property at Trasna Way on Saturday at around 9.15pm and attacked a woman and girl inside.
The teenage girl sustained serious stab wounds and was taken to hospital where she remains in a critical but stable condition.
A 41-year-old woman was also treated for stab wounds to her leg but has since been discharged from hospital.
A baby was present at the scene but was unharmed in the incident.
PSNI Detective Sergeant Keith Monaghan said: "This must have been a terrifying ordeal for those involved and we are determined to find the men responsible. We have several lines of enquiry which we are progressing at this time but I would ask anyone with information or who noticed any suspicious activity in the area to contact detectives in Enniskillen and pass that information on."
Alliance Fermanagh representative Matthew Beaumont said whoever carried out an attack in Lisnaskea needs to be caught quickly.
"This attack in Lisnaskea, carried out by men carrying machetes, is to be condemned in the strongest possible terms. Whoever was responsible for this horrific attack must be caught quickly and face justice."
"I hope the two females injured make a full and speedy recovery. This must have been a terrifying experience for them."