Beleaguered commuters from Brighton who have suffered years of delays on Southern and Thameslink have been warned that the main line will close for two nine-day periods for engineering works.

Network Rail and the train operator, Govia Thameslink Railway, urged passengers in Sussex to plan ahead for what they described as a “once-in-a-generation” upgrade to the southern end of the line.

The work, due to take place in October and in February 2019, will close the track south of Three Bridges, near Gatwick airport, to Brighton and Lewes. It is the centrepiece of a £300m upgrade programme to replace or upgrade track, drainage, power and signalling on the line, which is used by 300,000 passengers a day. Replacement buses will operate but the work is likely to add up to an hour to journeys.

Network Rail defended the timing of the work, due to take place over half-term holidays when passenger numbers are lower. John Halsall, the managing director of the Network Rail south-east route, said: “This is a long-overdue upgrade to one of the most unreliable parts of the south-east’s rail network. Southern and Thameslink passengers deserve better and this work will help us deliver that for them.”

He said the alternative to the two nine-day periods of closure would be 84 weekends. “Clearly, that’s not acceptable to passengers or the region’s economy – but neither is doing nothing.”

Keith Jipps, GTR’s infrastructure director, said: “We’ll be ensuring there are multiple options for passengers to make their journeys, including alternative transport to other rail stations and with other train operators. However, passengers need to know that they will have significantly longer journeys over this period of time.”

Caroline Lucas, the Green party MP for Brighton Pavilion, has demanded free transport for passengers and refunds for season ticket holders during the work. She said: “Passengers using this line have faced years of chaos and will welcome improvements, but it’s absolutely vital that such upgrades are done in a way which minimises disruption.”