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A “systems issue” at the ATO’s end on the last day of enrolment caused frustration for entities that tried to log in but were locked out and could not access the portal. 
Credible sources confirm that applicants should apply to the ATO on an individual basis to resolve their issue.
The question that’s circulating in everyone’s mind: Is there any extension?
The legislation states that if the entity elects to participate in the JobKeeper scheme, it must notify the Commissioner by the end of the relevant JobKeeper fortnight. In the past, the Commissioner used his deferral powers to grant an extension until the 31st of May for entities wanting to register for the payments for April and May i.e. fortnights 1 to 4.
The Commissioner is using his deferral powers again and has now extended the enrolment period for employers who are first enrolling in the JobKeeper scheme from June 2020 onwards to the end of the month in which the employer’s entitlement to the scheme arises.
For example, if an employer’s entitlement for the scheme arises in June 2020, the employer now has until 30 June 2020 to complete the JobKeeper enrolment instead of the relevant fortnight.
This latest development buys some additional valuable time for many businesses who wish to participate in the scheme and may have otherwise missed out.
The ATO has also given an extension to eligible entities that paid its employees on a monthly basis and may not have allocated the monthly payments in a reasonable way to ensure the payment made is at least $1,500 per fortnight. There may be circumstances where the allocation may not be reasonable because the work performed by the employee may significantly differ between the two fortnights.
This extension will be in place until the end of June and will enable entities to correct payments going back to JobKeeper fortnights ending in April and May.
For further guidance, please refer to the following:
https://www.ato.gov.au/General/JobKeeper-Payment/In-detail/JobKeeper-key-dates/#JobKeeperfortnights
https://www.ato.gov.au/general/jobkeeper-payment/employers/paying-your-eligible-employees/