Three of Africa's most dangerous Islamist militant groups are striving to co-ordinate their operations and represent a deepening threat to security on the continent, the US has warned.

General Carter Ham, head of the US military's Africa Command, said there were signs that Boko Haram in Nigeria, al-Shabaab in Somalia and al-Qaida in the Islamic Maghreb were sharing money and explosive materials and training fighters together.

"Each of those three organisations is by itself a dangerous and worrisome threat," Ham told an African Centre for Strategic Studies seminar in Washington. "What really concerns me is the indications that the three organisations are seeking to co-ordinate and synchronise their efforts – in other words, to establish a co-operative effort amongst the three most violent organisations … And I think that's a real problem for us and for African security in general."

Al-Shabaab is active in Somalia and has been blamed for attacks in Kenya. Last year, the group, which is allied to al-Qaida, claimed responsibility for the death of the Somali interior minister, Abdi Shakur Sheikh Hassan. It has, however, suffered setbacks in recent months.

Last month, the US classified three of the alleged leaders of Boko Haram, an Islamist sect based in remote north-east Nigeria, as "foreign terrorists", but it declined to blacklist the organisation to avoid boosting the group's profile internationally.

Al-Qaida in the Islamic Maghreb (AQIM), an affiliate of al-Qaida based in north Africa, is mainly a criminal organisation operating in the Sahel region. It kidnaps westerners for ransom and fuels Africa's drug trade, according to intelligence officials.

US and regional officials fear that a power vacuum in northern Mali after a military coup in March may open an expanded area of operations for Islamist militants. Some western diplomats talk of the country becoming a "west African Afghanistan".

Ham, addressing senior military and civilian officials from Africa, the US and Europe, said AQIM was operating "essentially unconstrained" throughout a large portion of northern Mali, where Islamists have imposed an extreme version of sharia law.

He added: "Most notably I would say that the linkages between AQIM and Boko Haram are probably the most worrisome in terms of the indications we have that they are likely sharing funds, training and explosive materials."

Africa Command has its headquarters in Germany. Its actions vary from the use of drones against al-Shabaab to the training of armies in various countries. Ham insisted that the US, which has about 2,000 troops in Djibouti, is not planning to expand its military role on the continent. "A large permanent presence in the continent of Africa is not, I think, what any of us desire."

A 100-strong US special forces contingent assisting in the hunt for the Ugandan warlord Joseph Kony also comes under Ham's command. He said: "This is an African-led effort. It is the African Union increasingly taking a leadership role with a little bit of support from the United States military. We think that is the right approach."