After a long and heated courtship, which saw both of the energy companies launch hostile takeovers for each other, the pair announced in April they had reached agreement on a $6.8 billion deal.
The deal sees Alinta acquire AGL's infrastructure business Agility for $6.45 billion to become the country's biggest energy infrastructure company with $14 billion in assets under management.
And AGL takes an initial 33 per cent of Alinta's West Australian retail and co-generation business, making it Australia's largest energy retailer.
But the Australian Competition and Consumer Commission (ACCC) has now raised concerns that Alinta's expanded presence in gas transmission in NSW could be anti-competitive.
In a statement of issues released on Friday, the ACCC said the deal would give Alinta a "substantial interest" in both of the key pipelines that feed gas to Sydney - the Eastern Gas Pipeline (EGP) and the Moomba to Sydney Pipeline (MSP).
The regulator said it believed "any degree of common ownership of the pipelines will have significant competition effects in the market for supply of wholesale gas to the south-eastern region of NSW (including Sydney)".
ACCC chairman Graeme Samuel said the deal did not set out structural separation of the gas transmission assets and Alinta had instead proposed behavioural commitments to ensure management of the assets was kept separate.
"Although Alinta offered undertakings to the ACCC in relation to this proposal, the ACCC has decided that competition concerns remain," he said.
Alinta chief executive Bob Browning said the company was disappointed the ACCC had taken issue with its acquisition of AGL's infrastructure assets, especially since it had spent the last three months in co-operative discussions with the regulator.
"As part of those discussions, we amended our original behavioural undertakings to take into account the concerns of the ACCC," he said.
"While we believe that the undertakings Alinta has made to date are broad and sufficient, we will continue to work with the regulator to determine how we can further strengthen these undertakings."
Browning said both Alinta and AGL remained committed to the merger deal.
At the close of the deal Alinta will have a 30 per cent stake in the MSP and a 20 per cent stake in the EGP and 100 per cent control of the companies that run the two pipelines.
Intersuisse energy analyst Peter Arden said resolving the standoff between Alinta and the regulator could be difficult.
Arden said Alinta had built its reputation on wringing growth out of underperforming assets and liked to have a stake in the operations it was running.
"In the growth phase they want to control it and do things with it and get the benefits, that's where they make their money, so that's going to be tricky," he said.
For legal reasons the hostile bids Alinta and AGL made for each other in the heat of battle remain open, although both boards are recommending shareholders take no action.
The ACCC has also ruled on those two deals, giving the AGL bid for Alinta the green light, but raising concerns over the Alinta bid for AGL.
AGL and Alinta are currently hammering out the final details of their merger deal and hope to have it approved by shareholders at meetings in September.
Source: AAP NewsWire