But she argues turning migrants away at the borders could violate European regulations, and potentially increase pressure on countries such as Italy and Greece.
"We must not contribute to weakening the European Union and purely national measures setting the tone again in Europe", said Merkel's spokesman, Steffen Seibert.
After Merkel nixed Seehofer's plan, the situation escalated into a war of words that pitched the conservative sister parties against each other.
Merkel is keen to avoid unilateral steps taken by the state, annoying the other countries-members of European Union and further weaken efforts towards a common migration policy for EU.
Her open-door policy has received intense backlash and is often credited for the rise of Alternative for Germany, a far-right, anti-immigrant party.
Commentators in Germany have noted that the spat is one of the biggest crises for Merkel, who was recently elected for a fourth term with only a narrow majority. But that would also lead to the collapse of her government, which has been in power for less than 100 days, and would nearly inevitably end her chancellorship.
Merkel's authority and the future of her alliance are at stake with Bavarian conservatives and Social Democrats (SPD) at a time when divisions within Europe have come to a head over a ship carrying migrants that was refused entry to Italy.
Rudy Giuliani says Trump might use pardons to ‘clean up’ Mueller investigation
However, hours after the comments spread like wildfire, Giuliani responded and seemingly backtracked from his original comments. The internal report reviewed one of the most controversial chapters of the 2016 election battle between Mr.
Merkel's coalition partner Social Democratic Party (SPD) had always been critical of plans to increase the country's defense budget, and disputed NATO's goal that each member should spend 2 percent of its national output on defense.
Merkel has proposed that asylum seekers already rejected by Germany could be turned back at the border.
The CDU executive committee is solidly behind the chancellor -at least that is what Schleswig-Holstein State Premier Daniel Günther told the daily Neue Osnabrücker Zeitung. He complained that, in this week's standoff, a senior CDU official had portrayed his party as "provincial lords who don't understand the European idea". Germany has received a disproportionate number of refugees from or European Union countries - over a million and a half for two years - and aims to make community partners also take ir part. "Asylum tourism must end".
"The task of governing our country is not an episode of Game of Thrones, rather a serious matter", he tweeted on Friday. "Those involved should not forget that".
Ms. Merkel's weekend decision to veto a plan by her interior minister aimed at controlling and reducing illegal migration-and the minister's refusal to back down-has shattered an uneasy truce between conservative backers and opponents of her liberal asylum policy.
Veteran CSU politician Hans-Peter Friedrich fueled the discussions, stating in an interview on German television that his party "stood united behind Interior Minister Horst Seehofer" in the row with its allies, but there were "no demands to end the cooperation with Angela Merkel".