U Soe Maung said the protest had been accompanied by photographs of Chinese nationals who had entered Myanmar illegally to extract the timber and minerals.
He said the photographs were taken by employees of the Ministry of Environmental Conservation and Forestry and members of armed ethnic groups that had signed peace agreements with the government.
The minister was responding to a question from Pyithu Hluttaw MP U Min Swe (Union Solidarity and Development Party, Daikoo Township, Bago Region).
U Soe Maung said the Ministry of Foreign Affairs in Yangon had summoned a Chinese embassy official on November 13 to lodge the protest.
Figures released by the Ministry of Environmental Conservation and Forestry show that 1,198 Myanmar and 414 foreigners were arrested for the illegal extraction of resources in border areas in the 10 years to 2014.
Ministry of Immigration and Population figures show that 33 foreigners were arrested for the illegal extraction of gold and timber from border areas and fishing illegally in Myanmar waters between March and April last year.
Figures from the Ministry of Mines show that 23 Myanmar were arrested between April and September last year for the illegal extraction of jade, gems and other minerals weighing about 22.5 tonnes and valued at more than K10.55 million.