The uncertainties are noted in a circular sent by Edinburgh-based Bowleven to shareholders. The company, led by chief executive Kevin Hart, is seeking approval for the proposed sale of stakes totalling 50% in the Etinde oil and gas permit off Cameroon to Russia's LUKOIL and Africa's New Age.
The company will hold a general meeting on 21 July where shareholders will vote on the proposed farm-out deal.
In the circular, Bowleven explained that completion of the deal was effectively conditional on the Petrofac oil services giant scrapping or amending the Strategic Alliance into which the companies entered in 2012 regarding the proposed Etinde development.
It said: "There will likely be a cost to the group's withdrawal from the Strategic Alliance in order to pursue the Transaction."
Bowleven may have to pay hefty compensation to Lukoil and New Age, depending on the outcome of talks between the firms. Bowleven warned :" If completion occurs at a time when the Strategic Alliance remains in place, there is a risk that the group may become liable to indemnify the purchasers ... which could materially adversely affect the roup's financial position."
Under the agreement signed in November 2012, Petrofac agreed to fund up to $500m of the first phase of developing Etinde for a return of 20% on its investment.
In the circular, Bowleven's chairman Ronnie Hanna wrote: "As a condition to completion of the transaction, the Strategic Alliance with Petrofac ... will require to be terminated (or at least amended such that the interests are released from its scope).
"Given that the group has no express contractual right to withdraw from the Strategic Alliance in order to pursue the transaction, the group has entered into discussions with the Petrofac Group regarding whether and, if so on what terms, the Petrofac Group might be willing to agree to any such withdrawal."
Petrofac said last week that the implications of the farm-out agreed by Bowleven for the Strategic Alliance had to be worked through. It did not elaborate yesterday. In the circular Bowleven said LUKOIL and New Age could agree to the farm-out completing while the alliance remains in force.
The circular noted uncertainties related to the plan to bring fields on Etinde onstream.
It said: "The proposed development of the Etinde Permit ... is a significant project with multiple risks and contingencies, including regulatory, funding, design, procurement, construction, development and midstream offtake risks."
Cameroon's President Biya has to approve the development.
The company noted it could only take a final decision on Etinde if other firms decide to build a fertiliser plant that would take gas from the permit.
Mr Hanna wrote: "The directors consider that the transaction is in the best interests of the company and its shareholders as a whole." They unanimously recommended shareholders vote for the deal.
Directors have said the farm-out will bolster Bowleven's balance sheet and allow it to devote more energy to exploration work, while retaining a 25% interest in Etinde.
Lukoil will acquire a 37.5% interest in Etinde under the farm-out. New Age will increase its holding to 37.5% from 25%.
The farm-out must be approved by a majority of votes cast by shareholders on an ordinary resolution at the general meeting.