The border will be closed indefinitely from midnight on Tuesday as confirmed cases of COVID-19 soar in Victoria.

It comes after two new cases were recorded in the Murrumbidgee Local Health District, believed to be in the Albury-Wodonga area.

Some exemptions are in place for medical professionals, and a permit system will operate for those living in communities which straddle both states.

But a spokesperson for Qantas and Jetstar confirmed there will be a reduced schedule of flights for the remainder of July, with the Sydney to Melbourne route to be the most affected.

Customers who have booked to be on a flight to Melbourne will be contacted by the airline with their options.

Multiple flights will continue each day, but the spokesperson said this will be "for essential travel only".

The Daily Advertiser reached out to Regional Express (REX) Airlines for comment on the proposed changes to flight times, but a response was not delivered before the time of publication.

Meanwhile the Melbourne to Sydney XPT train services will cease once the border closure comes into force.

"This XPT service will only operate between Albury and Central Station," the spokesperson said.

The last Melbourne to Sydney XPT service will depart Melbourne's Southern Cross Station at 7.50pm on Monday.

Meanwhile, the Sydney to Melbourne service departing Sydney's Central Station at 8.42pm Monday will only travel to Albury.

A one-off coach service will transport a number of customers from Albury to Melbourne, to complete the journey.

A spokesperson for Transport NSW confirmed that other services would be assessed for operation between NSW and Victoria.

"Special conditions will be in place for freight operations and logistics as well as other critical services," the spokesperson said.

"Provisions will also be in place for residents of border regions, including Albury-Wodonga."