Metro has made its two-phase fare increase one step more complicated: the 20-cent “peak of the peak” fare surcharges will go into effect only on the afternoon rush, not the morning one, come Monday.

The transit agency said Thursday — just days before the second round of fare increases are scheduled to take place – that its fare gates do not have enough memory to accommodate the new “peak of the peak” fares for both commutes, plus handle its all-day pass. It called the problem “unforeseen system programming limitations.”

So it decided to take Phase Two in two steps. Starting Monday afternoon, riders who enter the Metrorail fare gates between 4:30 p.m. and 6 p.m. will pay 20 cents extra on top of the already higher peak commute fares.

The transit agency hopes to institute the same surcharge for the morning commute – from 7:30 a.m. until 9 a.m. — by the end of the month, though no exact date had been set, said spokesman Reggie Woodruff.

For riders, the snag means good news for the pocketbook. But it may not be good news for Metro as it means about half the anticipated revenue boost it planned for the first month.

That’s why the transit agency didn’t just wait to start both halves of the program at once, Woodruff said. “We aren’t postponing it because we simply need the revenue,” he said.

So a recap of what’s happening:

On Sunday: Rail riders who use paper farecards will pay 25 cents more per rail trip. Though Metro had initially called it a “discount” for SmarTrip riders, the agency acknowledged that it’s actually an extra charge for paper farecard users on top of the recent fare hikes. SmarTrip users will pay the same amount.

Metrorail passes – including the short-trip pass, the fast pass and the transit link card – will increase in price to $32.35, $47 and $102, respectively.

On Monday afternoon: Peak of the peak fares surcharges of 20 cents will begin for rail riders entering a fare gate between 4:30 p.m. and 6 p.m. (Riders who enter before then yet exit during that window will not face extra charges, since it could penalize riders delayed by service problems.)

End of the month: The morning phase of the “peak of the peak” commute is slated to begin, though no date has been determined yet.

Aug. 29: SmarTrip farecards will drop in price from $5 per card to $2.50.