The Police Road retarding basin turned to a lake and water rose to within metres of the road when 82millimetres of rain fell in Scoresby on December 21 and 22.

The rainfall was well short of the 400-millimetre rainfalls that created Dandenong's one-in-30-year floods.

Flood researcher Alan Hood, who sounded a warning about the roadway with waterways expert Geoff Crapper in the Journal two years ago, said EastLink's design could lead to flooding upstream into properties north of the site.

He said the tollway, being built on an embankment that passes under Wellington Road, could act as a dam, impeding floodwaters and causing build-ups upstream.

"EastLink have built the freeway as a levee, when the correct structure is an elevated roadway built on pylons."

Mr Hood said the December 22 rainfall was not a serious test of the floodway, such as the 406 millimetres of rain over several days that led to floods in Dandenong in 1934.

"The embankment is holding back water even when the water hasn't risen over Wellington Road bridge ... if there were falls of 180 millimetres over 24 hours, that's the sort of rain that could come close to houses north of the road."

Mr Crapper said the December 22 rains were less than half the 2005 rainfall that first alerted him and Mr Hood to the flooding risk.

"It's the most significant thing since earthworks started with EastLink. But there'd need to be four times the rainfall for there to be a major impact."

A Thiess John Holland spokeswoman said the road section had been designed after "extensive modelling" to ensure the drainage could cope with heavy rain.

She said culverts built for Corhanwarrabul Creek and a bridge built across Dandenong Creek south of Wellington Road were "appropriately sized" to accommodate a one-in-100-year flood event.

"Modelling, which was been extensively checked by Melbourne Water and the independent reviewer, has shown that flooding for a one-in-100-year event will be no worse than what would have occurred prior to the construction of EastLink."

Scoresby Liberal MP Kim Wells said he would approach EastLink to ensure any concerns of flooding around Wellington Road was addressed.

"We would expect with the construction of a multibillion-dollar infrastructure project that there are no longer-term effects because of creeks and rainfall."