The troubled Tory took to her website to make a lengthy statement about the claims made by ex-staffer Arianne Plumbly – only to delete it about an hour later.
In it she reiterated her desire to continue in office and pledged to put the "distraction" behind her and "continue to serve constituents with determination".
In the statement, Ms Allan said: "Most employers have difficulties with staff at some point and MPs are no exception.
"While it was certainly human to be frustrated and exasperated by Arianne's conduct, it was wrong to express that frustration as I did, and I have apologised for this.
"Meanwhile, as the MP for Telford, while this has been a distraction, I will continue to serve my constituents with determination.
"We now have a strong, loyal and motivated team in Telford and in Parliament.
"We are able to get on with the job of attending to the needs and concerns of Telford people, which must always be the first priority for me and any member of my team."
Ms Allan has been under fire since publishing an email on Facebook which she said was sent to her following her decision to vote in favour of air strikes on Syria in the Commons.
She was accused by "Rusty Shackleford", an alias of Adam Watling, son of Telford & Wrekin senior councillor Paul Watling, of faking a death threat by adding the words "unless you die" to the email.
She said that was a "disgraceful slur" and said the post was a combination of two threatening emails she had received on the matter.
But calls were made for her to resign or be sacked and the hashtag #sacklucyallan trended briefly on Twitter.
Ms Allan deleted her social media accounts – only to make a brief return to publish a near 1,000-word post attacking a small group of Labour councillors in Telford and labelling them "bully boys".
Last week Ms Plumbly, a Conservative councillor on Oakengates Town Council, made public voicemails her former boss had left on her answerphone after she was signed off sick for four weeks by a doctor for stress.
In the voicemails Ms Allan appears to accuse Ms Plumbly of taking a computer from the office without permission, questions her illness and suggests she has an "alcohol problem".
Ms Plumbly has also called for her to resign.