The news comes in the week that Parliament President Antonio Tajani set up an ad-hoc working group to finalise a revision of MEPs' expenses and a week after journalists published findings of an investigation into how MEPs spend their so-called general expenditure allowance.
Helmer's resignation was announced in a Parliament notice published in Strasbourg on Tuesday. No explanation was given for Helmer's decision to resign midway through the European parliamentary term and after an 18-year career as an MEP.
The Guardian, however, reported that the veteran Helmer faces a bill close to €115,000 for illicitly employing a Ukip party worker, Paul Oakden, as his assistant. Oakden's contract has already been suspended.
MEPs are banned from hiring full-time assistants who have jobs in national political parties. Paul Oakden, says the Guardian, was employed as Helmer's assistant, while also working as Ukip Chair.
Parliament reportedly began its investigation last year and is due to send Helmer a formal letter for recovery because they are not satisfied with his explanations of an administrative misunderstanding.
It is believed that Helmer can appeal to the European Court of Justice in Luxembourg to contest the repayment demand, but if he loses, Parliament can recover the money from a possible €159,000 transitional allowance that the MEP is entitled to for two years after stepping down.
Speaking at a news conference in Strasbourg on Tuesday, S&D leader Gianni Pittella said he supported anything that would lead to greater transparency on the issue of MEP expenses.
On Wednesday, Helmer, formerly a member of the Tory party, did not respond to press calls and a European Parliament press office told this website it does not comment on individual cases.
But the spokesperson added, "MEPs' assistants are paid out of the European Parliament budget for work that is strictly related to the exercise of the mandate of a member of the European Parliament.
"Whenever the financial administration have serious questions about the actual work performed by an MEP assistant (that is, if the work performed is really related to the European mandate), they will ask the MEP concerned for clarifications and justifications.
"In cases where these justifications are not forthcoming, the assistant's contract may be suspended. Should clarifications still not be forthcoming, the administration may reclaim the funds for which no justification of work has been provided."
The new working group looking into MEP expenses is not linked to the Helmer case but a Parliament spokesperson said the revision will aim to "clarify and strengthen the existing rules and good practices."
It comes after Parliament passed a resolution in April which called on the Secretary-General to submit to the bureau a more precise list of expenses defrayable under the general expenditure allowance (GEA).
The revised list will be submitted for adoption to the bureau by the end of the year.
The ad-hoc working group is composed of MEPs David-Maria Sassoli; Rainer Wieland; Ryszard Czarnecki; Pavel Telicka Dimitrios Papadimoulis; Ulrike Lunacek; Elisabeth Morin-Chartier and Vladimir Manka.