The drugs include chlorambucil and busulfan - used to treat leukaemia.
The Commission said it was looking at claims that Aspen imposed "very significant and unjustified" price hikes.
The company confirmed an investigation was under way.
In a statement, Aspen said it was not currently in a position to comment on the proceedings but that it took compliance and competition laws very seriously and would work constructively with the EC.
Investigators will look closely at the pricing of key medical ingredients such as melphalan, mercaptopurine and tioguanine, used to treat cancers of the blood and immune systems.
Drugs involving these ingredients are sold under different formulations and different brand names.
South African company Aspen bought the rights to these from British company GlaxoSmithKline, after the patents expired.
According to figures reported in the Times, the price of the leukaemia medicine busulfan increased from Â£5.20 to Â£69.02 per pack in England and Wales after this deal.
Commissioner Margrethe Vestager said: "When we get sick, we may depend on specific drugs to save or prolong our lives.
"Companies should be rewarded for producing these pharmaceuticals to ensure that they keep making them in the future.
"But when the price of a drug suddenly goes up by several hundred per cent, this is something the commission may look at.
"More specifically, in this case, we will be assessing whether Aspen is breaking EU competition rules by charging excessive prices for a number of medicines."
The Commission said it was also looking at information suggesting that in order to impose price hikes Aspen had threatened to withdraw the medicines in some countries that were not receptive.
Aspen has previously been investigated by the Italian competition authority, which ruled that the company had fixed unfair prices with increases up to 1,500% for life-saving and irreplaceable drugs used to treat children and elderly patients.
In a statement the authority said: "The negotiation strategy adopted by Aspen was so aggressive as to reach the credible threat of interrupting the direct supply of the drugs to the Italian market."
In the UK new legislation is being introduced which gives the health secretary power to challenge drug pricing.
The European Commission has launched an investigation into claims that drug company Aspen Pharma excessively increased prices of five life-saving cancer medicines.