Detective Sergeant Andrew Raven, of the Warrnambool police crime investigation unit, said the men - a 64-year-old from Altona Meadows and a 47-year-old from Werribee, were arrested just before midnight on Tuesday.

The arrests were made at Pittong, between Linton and Skipton.

The investigation has involved Warrnambool detectives and tasking unit members as well as uniform officers from both the Corangamite and Ararat region districts.

"This is part of an ongoing investigation into the theft of wool," Detective Sergeant Raven said.

The men were charged with nine counts of burglary, six thefts, handling stolen goods and drug offences.

They were found with ice believed to be for personal use when arrested.

"Going back a number of months there have been break-ins at rural properties and sheds," Detective Sergeant Raven said.

"About 35 bales of wool, valued at $70,000, have been stolen. At one farm alone there were 18 bales stolen."

The average price for a bale of wool last year was more than $2000.

The thefts happened at Ararat, Westmere, Lismore, Skipton, Pura Pura and Vite Vite in the Lake Bolac district, south-west of Ballarat.

None of the wool has been recovered.

The 47-year-old Werribee man appeared briefly in Warrnambool Magistrates Court late on Thursday.

He did not apply for bail.

The court heard the co-accused from Altona Meadows would not appear in court as he had been rushed to hospital following a medical emergency.

Lawyer Amanda Chambers said he had type two diabetes, schizophrenia, chronic psychosis and ADHD.

She said he was also withdrawing from daily methamphetamine use.

The pair were remanded in custody until September 19.

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